2. Water and Sediment Quality Background Clean water provides many beneficial uses of California’s waterways, which include swimming, fishing, and the protection of aquatic life. State and federal laws have been enacted to protect these beneficial uses. Because waterway impairment is often caused by processes and activities at a watershed scale, watershed assessment is necessarily linked to understanding and protecting water quality. Numerous state programs exist to help protect our waterways, including the TMDL (Total Maximum Daily Load) Program, the National Pollution Discharge Elimination System Permits (NPDES), and Timber Harvest Plans. A TMDL is developed when a waterbody fails to meet its beneficial uses. In these cases, a plan is developed to reduce the pollutant loading. NPDES permits are issued by the State Water Resources Control Board (SWRCB) to dischargers such as cities which release stormwater, Caltrans, as well as industry, all in an effort to regulate the amount of contaminants released into waterways. Timber Harvest Plans and Sustained Yield Plans are approved by the California Board of Forestry and consider the impact of logging operations on the waterways within forests used for resource extraction. All are regulatory efforts to protect water quality. Monitoring water quality is one way of assessing watershed conditions and the effectiveness of regulatory and management efforts. A combination of geographic knowledge of your watershed, identification of the roles of influential drivers and processes (e.g., water diversions, storms, urbanization, agriculture), and measurements of water and sediment quality can provide a good indication of conditions and potential risks to your watershed. This chapter reviews:

• how to develop a water quality monitoring plan, • identifies a variety of commonly-measured water quality parameters, • describes techniques for making the measurements, • reviews methods for analyzing the data.

In those cases when detailed methods are readily available; links are provided to these resources within the text. The CWAM website (http://cwam.ucdavis.edu) lists additional online resources for information about monitoring water quality.

Chapter Guide Background 1 2.1 An Overview of Issues to Consider 2 2.2 Monitoring Methods for Common Water Quality Parameters 4 2.3 Methods for Measuring Contaminants in Water and Sediment 17 2.4 Analyzing the Data 24 2.5 Conclusions 36 2.6 References 37 Appendix 39

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2.1 An overview of issues to consider when developing a water quality monitoring program Careful planning will enable you to get the most from the monitoring effort you undertake. The following basic questions should be answered in developing a water quality monitoring program or evaluating existing data. 2.1.1. Where Should We Monitor? Three basic approaches can be used for determining sample sites. The first approach involves selecting sites based on your judgment, and is sometimes referred to as judgmental or directed sampling. You might select sites you suspect are impacted or degraded as a consequence of human activities; this approach is sometimes called “hot spots” monitoring. If you decide to monitor the “hot spots” you will be able to get a good understanding of conditions in specific areas about which you have concern, for example, below a wastewater treatment plant or downstream from a new housing development or a road. However, this information may not provide a good “overall picture” of the watershed since the sampling sites were selected to tell you something about activities associated with specific land uses or activities. This design ensures that your judgment is the basis on which the sites are selected. The second approach is to randomly select sites within the watershed If you are seeking an overall picture of water quality, then randomly selecting sites might be the best approach. Water samples collected from randomly selected sites will provide an overall characterization of the waterway. The data collected will be representative of the watershed as a whole, but not of any specific locations and activities. One way to identify random sites is to generate sample points using a GIS. The Hawth Tools, a free set of ArcGIS extension, have the ability to generate random points on a map of the watershed. In this way, you can have confidence that any personal knowledge or bias did not influence the selection of the sampling sites. The third approach is to collect samples from the bottom of each tributary of the main waterway and at or near the mouth of major tributaries and at the base of the watershed. This approach facilitates collecting water quality information that sums all the potential constituents and contaminants in the tributary and originating from the tributary watershed. This approach does not focus on hotspots but neither is it a completely random sampling method. It attempts to provide a picture of water quality within a creek or river and its tributaries without extensive sampling which can be very costly. A modification of this approach is known as the stratified random sampling design. Using this design, you would select a category, such as each tributary in the watershed, then randomly select sites within each tributary. This modified approach offers the benefits of ensuring that key waterways in the watershed are examined, yet the exact sites are randomly selected to ensure an unbiased assessment that provides an overall picture of conditions. If you are planning to use the water or sediment quality data for the development of watershed indicators, then randomly selected sampling sites is generally the preferable approach. The issue of sampling design is discussed in greater detail in the US EPA document Guidance for Choosing a Sample Design for Environmental Data Collection (http://www.epa.gov/QUALITY/qs-docs/g5s-final.pdf).

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2.1.2. When to monitor? Some water quality parameters can vary daily and seasonally, or be affected by storms. For example, DO concentration is naturally higher in colder water than in warmer water due to the higher solubility of oxygen in cold water. Chemical contaminant concentrations in stormwater discharge are usually highest after a storm. These variations should be considered in developing the monitoring program. Another issue to consider is the length of time that a condition or contaminant is likely to persist. Frequently, not only the concentration or level of a water quality constituent presents a problem, but the duration of the exposure can be just as important. For this reason, the US EPA has established criteria for acute and chronic exposure; the acute or short-term exposure criteria values are higher than the chronic ones. Gaining knowledge of both the concentration of the contaminant and the duration of the exposure is important in developing a monitoring program. 2.1.3. What to monitor? Most water quality monitoring programs focus on collecting water samples. However, sediment samples can be just if not more important to collect, depending on the constituents you are interested in monitoring. Many hydrophobic compounds, those that are poorly soluble in water, cling to fine particles in the streambed and can be detected only in extremely small quantities in the water column itself. However these contaminants could have significant effects on aquatic life either through direct contact with benthic organisms such as invertebrates or indirectly, by moving up the food chain. Before determining what type of media will be evaluated, it is wise to assess which of the contaminants of interest are likely to be associated with sediment and/or water. 2.1.4. How to Monitor? The method of sample collection is another important step in developing a monitoring program. The goal is to obtain a representative sample. In most cases, this involves collecting numerous samples from the same location. Further, the site in the water column or streambed from which the sample is collected and how it is collected are important considerations. It is also important to collect and transport the samples in a fashion that will protect them from degradation and prevent the chemical transformation of the constituents. . If you plan to transport the sediment or water samples, special consideration should be given to preventing degradation of the constituents due to exposure to heat or air as well as the introduction of contamination during handling. Finally, it is important to keep a careful record of the characteristics of the site itself. Record everything about the monitoring event at a site that seems important (e.g., date, time of day, water depth, water depth relative to previous monitoring). These and other issues should be thought through prior to beginning a monitoring program. 2.1.5. How to Analyze the Data Typically, most water quality data are compared to some standard, criteria, or reference value. Reference values reflect the background level of a constituent or the concentration in the least impacted waterways of the region. Water quality criteria have been set by the US EPA and the State and the Basin Plans for each Regional Water

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Quality Control Board for protection of beneficial uses. At a minimum, the data you collect should be summarized with descriptive statistics, such as means and confidence intervals, or standard deviations. If sufficient data has been collected, then more formal statistical analyses can be performed. Examples are provided towards the end of this chapter. Consider Sample Size Ahead of Time Sample size is an important data analysis issue that should be considered prior to collecting data. If possible, consideration should be given to the number of samples required to detect a difference, if one exists, and with what degree of confidence and precision. Based on previous data, you can calculate the amount of new data you will need in each location to achieve confidence in your conclusions given the variation you have found from previous sampling efforts. Using data from some historic or preliminary collection effort, a sample size calculation can be performed to ensure an adequate number of sites, providing greater confidence in your results. The details of sample size or power analysis were provided in Chapter 1 of this volume. An informative discussion of the topic, Power Analysis and Sample Size Determination, is also available online, written by a physician at UCLA. The article is posted at: http://www.saem.org/download/lewis4.pdf. Many free sample size calculators are also available online. To use them, you must have some estimate of the variability that exists within the data. One example of this type of software is a program developed by Russ Lenth, a professor at the University of Iowa, and available at: http://www.cs.uiowa.edu/~rlenth/Power/. 2.2 Monitoring Methods for Common Water Quality Parameters

In this section, a variety of water quality parameters or conditions that can be measured, including information on various sampling and analytical techniques, are reviewed.

2.2.1. Water Temperature

Because of its great impact on aquatic life, water temperature is an important component of a watershed assessment. Temperature affects the distribution, health, and survival of aquatic organisms. While temperature changes can cause mortality, it can also cause sub-lethal effects by altering the physiology of aquatic organisms. Temperatures outside of an acceptable window affect the ability of aquatic organisms to grow, reproduce, escape predators, and compete for habitat. For certain organisms, their optimum temperature range may be very narrow and for others, very wide. The optimum temperature range can vary not only among species, but also for different life stages of the same species. For example, the temperature threshold for impairment of chinook salmon smolts is 12 oC while a higher temperature, 21 oC or 70 oF, is the threshold for inhibiting the spawning migration of adults (US EPA, 2001). Knowledge of the temperature range for each life stage of each species of concern is an important part of the evaluation of potential temperature concerns. Scientists have found that water temperature can be highly variable within waterways and between seemingly similar waterways (Boyd and Kasper, 2004; Torgersen et al., 1999 & 2001). This variability can be associated with both natural (e.g., springs) or

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human-induced (e.g., reduced canopy cover) factors. Spatial and temporal variations are additional factors to consider in developing a monitoring program. A reconnaissance-level survey of temperature during different times of day and over different seasons, on different waterways, can provide sufficient information to determine when and where to collect the data. The key to evaluating water temperature data is to compare local conditions to known standards that support aquatic life. Such standards are readily available for a wide variety of fishes. The US EPA has produced an excellent reference source for salmonids: A Review and Synthesis of Effects of Alteration to the Water Temperature Regime on Freshwater Life Stages for Salmonids, with Special Reference to Chinook Salmon, published in 1999 (http://www.critfc.org/tech/EPAreport.htm), or the more recent document, A Summary of Technical Literature Examining the Physiological Effects of Temperature on Salmonid, 2001. Both are available for downloading from the US EPA Web site. Information on the temperature requirements of other species is also readily available on the web or at a university library. In the Appendix to this chapter is a list of commonly used water temperature standards for salmon. Temperature standards for California waterways are largely basin-wide and aimed at minimizing changes in temperature rather than maintaining an absolute value. This makes comparison of measured waterway temperatures in your watershed to a benchmark challenging. However, there are studies of the effects of temperature on fish, especially salmonids, which you can use to develop standards for your watershed or region. Some of these studies are:

• Sullivan et al., 2000 (http://www.sei.org/downloads/reports/salmon2000.pdf). • A review by UC Davis scientists of temperature effects on Central Valley salmon

and steelhead (http://cwemf.org/Pubs/TempReview.pdf), • Work by members of the University of Washington Columbia Basin Research

group on temperature sensitivity of salmon in the Pacific Northwest (http://www.cbr.washington.edu/papers/beer-anderson2004.html),

• A forecast of global climate change effects on trout and salmon based on temperature effects (http://www.defenders.org/publications/fishreport.pdf).

I. Methods for Water Temperature Measurements (1) Manual measurement Because manual measurement of temperature requires that someone physically go out to take the reading, most measurements have been in the daytime, which may be appropriate when higher temperatures are a concern. In smaller waterbodies, and near the surface of larger waterbodies, diurnal fluctuations in temperature can occur with fluctuations in air temperature. So, measurements should be taken at the same time of day or preferably, at intervals throughout a 24-hour period. More frequent measurements will provide information to understand the average and maximum and minimum water temperatures Temperature can be manually measured using a hand-held alcohol/glass or digital thermometer. The thermometer is immersed in the water and given sufficient time to equilibrate (<1 minute) before a reading is taken. Measurements should be taken from the part of the waterway that represents the predominant condition (e.g., the main

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channel of multiple channels). Often the monitoring target is running water in a channel. However, you could also measure temperature along lateral and longitudinal sections of waterways to capture side pools and measurements at different depths for pools in waterways and in lakes/reservoirs/ponds. The basic considerations for measuring temperature manually are:

• If high temperatures are the reason water temperatures are monitored, consider measuring temperatures in late afternoon.

• Choose a spot where you will be measuring the dominant flow in moving water or near to the center for pond water.

• Immerse the measurement device well below the surface of running water (0.5 x water depth is best).

• In still or slow-moving water, consider taking at least 3 measurements at several recorded depths.

Resources for Additional Information: http://www.epa.gov/owow/estuaries/monitor/pdf/monitoring_manual.pdfhttp://www.swrcb.ca.gov/nps/docs/cwtguidance/312ip.pdfhttp://www.healthebay.org/assets/pdfdocs/streamteam/FieldGuide.pdf. (2) Automated measurement The use of an automated probe facilitates the collection of accurate information about the daily cycle of temperature, the daily average, and the extremes. These probes consist of small battery-powered wireless probes that are installed in the waterbody in a place that represents the desired condition over the sampling period and that can be periodically retrieved to download data stored in the device. Measurements are taken at pre-programmed intervals and can be periodically retrieved The basic considerations of measuring temperature with automated probes and data loggers are the following:

• The probe or remote device should be placed in the dominant flow/portion of the waterbody, one will remain underwater regardless of changes in typical flow pattern.

• Most remote wireless devices are small, so mark the spot carefully, either through large, carefully-placed stones, or by using an established station with a permanent pipe submerged in the water.

• Assess the optimal frequency of measurements, considering your objectives. Consider battery life conservation and data management . In some cases, you can collect an unwieldy amount of data. A frequency of 30 minutes has often been used successfully.

Information on calibrating thermometers is available from the Clean Water Team, http://www.swrcb.ca.gov/nps/volunteer.html; State Water Resources Control Board).

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2.2.2 Dissolved Oxygen Aquatic organisms use oxygen for metabolic processes and require concentrations above a certain level to survive and grow. Energy production is dependent on the availability of oxygen. When dissolved oxygen (DO) is less than 3 or 4 mg/L for warm water fish or 7 mg/L for cold-water fish, they are unable to extract sufficient oxygen from the water to support physiological functions. Their ability to catch prey is reduced, reproduction is negatively impacted, and a variety of other adverse physiological effects occur. The primary sources of oxygen in water are diffusion across the water surface and photosynthesis by aquatic plants. There are many waterways in California where DO concentrations are insufficient to meet the needs of all aquatic organisms. This condition is most frequently associated with increased “biological oxygen demand” from microbial metabolism or algal respiration at night when photosynthesis is not taking place. While plants only produce oxygen using the energy from sunlight, they consume it all the time. Oxygen is depleted from a waterway by microbial respiration and oxidation of reduced chemicals such as ammonia and sulfide. A variety of conditions that might alert you to the need to monitor DO in your watershed include: • Excessive algae and macrophyte growth is present in a stream. • Upstream reservoirs that release water from the bottom of the reservoir, where

oxygen concentrations may be low due to inadequate mixing with surface water and microbial action.

• Fish appear stressed or die in certain reaches of the waterway, especially in slow-moving water where re-oxygenation from the atmosphere may be limited.

• Previous measurements show low concentrations at certain places and during certain times of the day or over the course of a year.

• Water emits a foul odor. I. Method for DO measurement Measuring DO concentrations accurately is usually performed with an oxygen probe or chemical kit. Automatic samplers are also available, but require more frequent attention than temperature probes. Both of these approaches will be reviewed in this section. 1. Manual measurement of DO is the most common method and can be done with wet chemistry or an oxygen probe.

• Wet Chemistry

The measurement of DO using a chemical kit is based on the Winkler method. DO is chemically “fixed” in a complex with iodine, a stabilized form that can be stored for weeks. This complex is later dissolved with the addition of concentrated acid. Free iodine in solution is titrated with the addition of sodium thiosulfate. The volume of sodium thiosulfate added to completely titrate the free iodine is proportional to the amount of DO in the sample.

• Oxygen Probe

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A probes measure DO in water by measuring the electrons required for a chemical reaction on the surface of the electrode. The number of electrons required for the reaction is proportional to the concentration of oxygen in the water. The probe needs to be calibrated regularly. 2. Automated measurement of DO involves an oxygen probe (described above) that is connected with a cable to a data storage device and deployed in a waterbody. These devices can usually be programmed to take measurements during a set period (minute, hour, day) depending on need. The probes need to be serviced and checked every few days due to build-up of bacteria and algae on the active surface of the probe and potentially changing water levels. The probes also need calibration prior to each monitoring event. Consider measuring temperature at the same time as DO because temperature affects the saturation concentration of oxygen in water. II. Quality Control The same types of requirements that exist for temperature monitoring are true for DO. . In particular, the timing of DO measurements is important to consider because it fluctuates on a daily basis as well as throughout the year as the temperature and flows vary. Therefore, if DO cannot be measured with an automated sampler to capture the variation throughout the day, it should be measured at the same time every day. Another consideration is that if your use the Surface Water Ambient Monitoring Program (SWAMP) protocol for measuring temperature, DO, or any other parameter, the data can be entered into the SWAMP database to be shared with others. Developing a Quality Assurance protocol, known as a QAPP, is required in order to add your data to SWAMP’s database. This ensures that the methods are recognized as valid and permits comparisons of results from different watersheds. III. Sources for Additional Information The State Water Board’s Clean Water Team has an informative set of papers reviewing DO monitoring issues, posted at: http://www.swrcb.ca.gov/nps/docs/cwtguidance/311ip.pdf. 2.2.3. Nutrients Nutrients are essential for plant, microbial, and animal growth. However, when certain nutrients, such as nitrogen and phosphorus-containing compounds, are present in high concentrations in waterways, they can cause excessive algal and microbial growth which indirectly impacts other biota. Nitrogen availability can be an important factor controlling algal growth when other nutrients, such as phosphate, are abundant. If phosphate is not abundant it may limit algal growth rather than nitrogen. Ammonia is excreted by animals and produced during decomposition of plants and animals, thus returning nitrogen to the aquatic system. Ammonia is also one of the most important pollutants because it is relatively common but is also the most toxic, causing lower reproduction and growth, or death. The neutral, un-ionized form (NH3 )ammonia is directly toxic to fish and other aquatic life.

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Nitrate is the preferred nitrogen-containing nutrient for plant growth. Ammonia can be converted to nitrite (NO2 ) and nitrate (NO3) by bacteria, and then used by plants. Nitrate and ammonia are the most common forms of nitrogen in aquatic systems. Nitrate predominates in unpolluted waters. The most commonly-measured nutrients are nitrogen and phosphorous-containing compounds. These classes of nutrients originate from natural processes such as degradation of plant matter in streams, human activities, such as urban and agricultural runoff, effluent from wastewater treatment plants, and atmospheric deposition from auto and industrial emissions. They may be carried by air, surface and ground water, or attached to particles. Nutrients can originate from point sources, such as wastewater treatment plants, and non-point sources, such as agriculture and natural degradation. They are among the most commonly-measured water quality parameters. Human activities, such as the use of fertilizers, are usually the primary cause of excessive nutrients. Effluent from wastewater treatment plants as well as atmospheric deposition from automobile and industrial emissions can also be sources of nitrogen. Nutrients can also originate from natural processes such as degradation of plant matter in streams. They may be carried by air, surface and ground water, and are dissolved or attached to particles. Natural disturbances such as extreme weather events and fires can also contribute excessive nutrients to a system. Further, some waterbodies are naturally have highly concentrations of nutrients (i.e., more eutrophic, meaning more nutrient-rich and productive) than others. A concentration of phosphorus that is “normal” for one waterway might be excessive for another. Excessive nutrients can be toxic for a few reasons. In the majority of cases, the growth and subsequent decay of algae deplete the water of oxygen, causing the DO levels to fall below those needed to support aquatic life. In rare cases, high concentrations of ammonia can be directly toxic to aquatic organisms. The chemical form of ammonia is closely linked to its toxicity to aquatic organisms. Ammonia can occur with or without a hydrogen atom. When the hydrogen is associated with ammonia, the molecule has a positive charge and is unable to easily cross biological membranes to permit absorption into fish. Without the hydrogen atom, ammonia is in its un-ionized form and can easily pass through the membranes of the gills, causing nervous system toxicity and even death. I. Natural Contributions of Nutrients to Waterways Sources and Sinks of Nutrients Nutrients originate from natural processes such as degradation of plant matter in streams and human activities, such as urban and agricultural runoff, effluent from wastewater treatment plants, and atmospheric deposition from auto and industrial emissions. They may be carried by air, surface and ground water, and dissolved or attached to particles. 1) Agricultural Contributions Irrigated agricultural and confined animal facilities such as feed lots can produce runoff that can enter waterways and change the carbon, nitrogen, phosphorous, and mineral concentration in surface and ground water. If specific concentrations in discharges and

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the volumes of water discharge can be quantified, then the actual amount or “load” from certain areas or practices can be determined. 2) Urban Contributions Urban land uses are also important potential contributors of nutrients into waterways. Regulated municipal and industrial wastewater associated with urban areas can release nutrient-rich water. Excessive use of fertilizers can runoff into local streams. Utilities, automobiles, and industries produce exhaust containing aerosolized and particulate nitrogen pollution. Atmospheric deposition is harder to measure, but can theoretically be measured as “wet deposition” by collecting rainwater in urban areas and measuring the nutrient concentrations. Regulated dischargers must keep track of their production of nutrients and can be an important valuable source of technical data and information. 3) Natural processes and nutrient cycling In less-developed areas, natural processes can have as much influence on nutrient concentrations as direct inputs from human activities. For example, erosion and leaching of certain geological formations and soils formations will contribute nitrogen and other nutrients to waterways during natural erosion. In addition, aquatic and terrestrial plants can contribute large amounts of organic material including nutrients to streams, rivers, and wetlands during cycles of growth and decomposition. Fire may temporarily increase the contributions of nutrients from eroded soil and burned vegetation. Riparian and floodplain vegetation may decompose and contribute to local and downstream enrichment of nutrients.

Example: Malibu Creek – Algae and Nutrients Investigators in Southern California have found that benthic algae blooms are associated with intensive land-use. At water quality monitoring sites downstream from residential development, commercial areas, and a wastewater treatment plant, benthic algae levels were two orders of magnitude higher than at reference (undeveloped) sites. Investigators also found high concentrations of nitrates, soluble-reactive phosphorous, total dissolved phosphorous, and total dissolved nitrogen at sites downstream of developed areas. There was a strong correlation between land-development and nutrients and algal growth. From in-stream experiments with nutrient availability and measurement of light and flow, the investigators determined that multiple management measures would be needed to improve the waterway. For example, increased riparian forest cover would shade the waterway and deprive algae of light. Many-fold reduction in nutrient concentration would also be needed to limit algal growth. Busse et al., 2003. A survey of algae and nutrients in the Malibu Creek watershed. SCCWRP Technical Report #412. (ftp://ftp.sccwrp.org/pub/download/PDFs/412_algae_nutrients.pdf)

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Nutrient cycling process involving algae is natural, but the peaks and troughs of nutrient concentrations may be enhanced by human activities. Sometimes these natural fluxes are triggered or enhanced by human activities (e.g., algal blooms). For example, surface waters may be warmed by water management (e.g., diversion of natural flows), which may in turn contribute to increased growth of attached algae and aquatic vascular plants. This increased growth may temporarily reduce the nutrient concentrations in waterways when plants use up the nutrients as they grow. As the plants die off in the fall and winter, their nutrients may be returned to the water as particulates and dissolved material and may end up contributing to downstream nutrient cycles. Thus the cycling process involving algae is natural, but the peaks and troughs of nutrient concentrations may be enhanced by human actions. Baseline or natural input of nutrients can be measured in a sub-watershed that has low levels of human activities. The role of natural processes, such as in-stream plant and microbial action, should always be taken into account when considering nutrient concentrations and loads in watersheds and waterways. Measurements of both background and human-stimulated nutrient cycling and the seasonal and management-related changes in the cycling should be performed whenever possible. II. Measurements of Nutrients The two most commonly measured nutrients are nitrogen, as ammonia or nitrate, and phosphorus. These nutrients can be measured in different forms. 1. Measurement of Nitrogen Nitrogen is commonly measured as total nitrogen, ammonia, NH3 and nitrate. The most common method for measuring ammonia is the Salicylate Method, which can be purchased as a test kits. This method involves a color reaction of ammonia with hypochlorite (bleach) and salicylate (aspirin) to form a green-colored complex, which can be compared to standards. As with all analysis, fresh standards should be run periodically to calibrate the measurement at least every six months to verify your technique and the integrity of your chemicals. Since the amount of nitrogen present as ammonia is dependent on the water pH and temperature, it is important to measure these two parameters at the same time as ammonia. Because this method is not very sensitive, only high concentrations of ammonia can be measured this way.

Nitrate and nitrite are the two other forms of nitrogen measured most frequently. Nitrate is usually the most stable and is the form most often found in aquatic environments. Nitrite can be found in oxygen-poor waters. Nitrate is very difficult to measure directly, so it is converted to nitrite and the resulting nitrite concentration is then measured. The measurement gives the combined concentration of nitrite (if present) and nitrate. These measurements are based on the reaction of the two forms of nitrogen with a dye. More information on all three forms of nitrogen and their measurement is available at: http://www.swrcb.ca.gov/nps/cwtguidance.html#40

2. Measurement of Phosphorus

Phosphorus is a required macro-nutrient for green plants. If phosphate is not abundant it, not nitrogen, may limit algal growth. It is often a limited resource especially in fresh

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water systems. When naturally occurring levels become elevated algal blooms can occur, leading to oxygen depletion and fish kills. Phosphorus is frequently measured as orthophosphate, the form most readily taken up by plants. It can be measured with a wet chemical kit. The test kits for measuring orthophosphate also typically involves incorporate a colorimetric reaction with molybdenum, producing either a yellow or blue colored complex, depending on the method, which is compared to standards. The Clean Water Team Web site contains information on measuring ortho-phosphate. For both nitrogen and phosphorous monitoring, concentrations in many Californian waterways will be too low for most commercial test kits to detect. Exceptions to this are in urbanized watersheds, agricultural watersheds, and many low-elevation wetlands. Even at low concentrations, significant growth of aquatic plants can occur because of their efficient uptake of nutrients. For example, in the Yuba River, heavy growth of attached filamentous algae can occur at nitrate and phosphate concentrations similar to those found in Lake Tahoe (F. Shilling, unpublished observations). Since the detection limits of most kits will not be sufficiently low to detect the small quantities usually present in California waterways, you will need to work with a University, agency, or certified commercial laboratories that can measure lower concentrations if you suspect it is a problem. In addition to the information from the State Water Resources Control Board, another useful source of information for how to sample and analyze nutrients in water is the US EPA’s Volunteer Estuary Monitoring Methods Manual, posted at: http://www.epa.gov/owow/estuaries/monitor/pdf/monitoring_manual.pdf. Chapter 10 contains the methods for nutrients. Although this manual was designed for use in estuaries, the methods are the same for freshwater measurements as well. There is also the slightly older “Volunteer Stream Monitoring: A Methods Manual” (http://www.epa.gov/owow/) which contains easy-to-understand descriptions of sampling and measurement techniques for various nutrients. The Clean Water Team Web site also contains information on measuring ortho-phosphate. 2.2.4. Turbidity and Suspended Solids Turbidity is an easily-measured surrogate for the concentration of suspended solids in water. Sediment, algae, and organic matter are all considered “suspended solids” and can cloud the water, making it more turbid. Total suspended solids (TSS) is the direct measurement of particle concentration while turbidity is an indirect measurement that quantifies the diffraction of light caused by particles in the water. Turbidity and TSS concentrations have been recommended by the US EPA as useful indicators of water quality and are important measurements for a number of reasons. Increased turbidity and TSS are frequently indicators of erosion (e.g., of stream banks or fine material washing off of construction sites). This fine material can clog the gills of fish and benthic insects as well as serve as a carrier of pollutants and pathogens. I. Methods for Measuring Turbidity

There are a variety of ways to measure turbidity. One is to measure transparency or water clarity. This measurement is usually performed in lakes using a Secchi disk, a round disk with a black and white pattern. It is lowered into the water to a depth where the pattern is no longer visible and is well suited to measuring turbidity in lakes. In rivers

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and streams, the most common measurement is based on the ability of particles to scatter light or simply by weighing the particles. Light scattering or turbidity is measured with a small, hand held nephelometer that can be easily carried into the field. The degree of light scattering is recorded by the instrument as NTUs, or nephelometric turbidity units.

Concentrations of total suspended solids are measured in a laboratory by evaporating all the liquid in a water sample of known volume and weighing the remaining solids. Results are reports as mg/L water or parts per million (ppm).

A more detailed discussion of these and other methods for measuring suspended particles are contained in the Clean Water Team Compendium, posted at: http://www.waterboards.ca.gov/nps/cwtguidance.html in Section 3.1.5. Because not all suspended material causes light to scatter to the same degree, NTUs cannot be easily converted to suspended solids concentration (ppm) or vice versa. The relationship between to these two measurements can be developed on a stream by stream basis by collecting both measurements at the same time and plotting a regression relationship. Once this relationship is established for a particular waterway, nephelometric readings can be easily converted to ppm suspended solids. This relationship is important because much of the data in the scientific literature addressing the effects of turbidity on aquatic life are reported as ppm suspended solids. To be able to compare conditions in your waterway to those known to cause harm, you need to make this conversion. The following table is from the CWT Compendium’s summary of methods for measuring turbidity. It presents an overview; additional details can be found on their Website. For the table: cut columns “Code” and “Application”

• format text consistently • include notes below

Principal Method name

(Parameter, unit) Approx.

Cost* Labor Limitation Extent & Sources of Error

Transparency Murkiness (Note b) None 30 sec Not Applicable

Unknown

Transparency Secchi disk

(Secchi depth, cm)

~$30 2 min Need to deploy from

above Daylight

only

± 30%; Individual operator’s vision, Lighting, surface reflection, depth measurements

Transparency Transparency tube(Transparency,

cm)

$40 5 min Daylight only

± 30%; Individual operator’s vision

Length measurement,

deposition

Transparency

match

Dual cylinder (Jackson turbidity,

JTU)

$40 5 min Daylight only

± 40%; Individual operator’s vision,

quality of standard, volume

measurements

Light-scattering

Nephelometer (Turbidity, NTU)

$300 and up

10 min cal 1 min

Error variable, depending on

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measure instrument

Light-scattering

Automated Nephelometer

(Turbidity, NTU)

$1000 and up

Installation, calibration, download.

Fouling of light absorbing surfaces,

drift from the calibrated state

Gravimetric: Dry Weight

per volume of sample

aliquot (Note c)

Filtration for Suspended Solids of a sub-sample of water (TSS, mg/l)

$2000 and up

20 min Requires laboratory

facility

Error variable, depending on

operating procedures

Gravimetric: Dry Weight per volume (by water weight) of

whole sample

Filtration for Suspended Sediment

Concentration in entire water

sample (SSC, mg/l)

$2000 and up

20-60 min

Requires laboratory

facility

Error variable, depending on

operating procedures

Sinking Imhoff Cone Method

~$30 5 min(setup and read)

Requires cones

± 30%; Lighting, surface

identification,volume measurements

* - Costs for each test identified above are estimates only and include equipment costs. 2.2.5. Conductivity & pH Two other measurements that are frequently performed to evaluate overall water quality are conductivity and pH. I. Conductivity Conductivity measures the ability of water to conduct an electrical current, which is linked to the amount of salts in the water. The major salts that contribute to the measurement of conductivity are sodium, calcium, magnesium, and potassium; all positively charged ions. Other ions that contribute to conductivity to a smaller degree are sulfate, chloride, carbonate, bicarbonate, nitrate, and phosphate (Clean Water Team Compendium). Streams that run through areas with granite bedrock tend to have lower conductivity because granite is composed of more inert materials that do not ionize (pick up a positive or negative charge when dissolved in water). On the other hand, streams that run through areas with clay soils tend to have higher conductivity because of the presence of materials that ionize when washed into the water. Ground water inflows can have the same effects depending on the bedrock they flow through. Discharges to streams can change the conductivity. A failing sewage system would raise the conductivity because of the presence of chloride, phosphate, and nitrate; an oil spill would lower the conductivity (US EPA Water Quality Monitoring Guidance, posted at: http://www.epa.gov/owow/monitoring/monintr.html). The importance of the measurement relates to their impact on water quality for drinking, irrigation, and aquatic life. All plants and animals, including humans, have a range of acceptable levels of salts in water. Conductivity is measured in micromhos per centimeter (µmhos/cm) or microsiemens per centimeter (µs/cm). Distilled water has conductivity in the range of 0.5 to 3 µmhos/cm. The conductivity in waterways usually

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ranges from 50 to 1500 µmhos/cm, with the preferable range for fisheries varying between 150 and 500 µmhos/cm. Conductivity outside this range could indicate that the water is not suitable for certain species of fish or macroinvertebrates. Conductivity can vary with temperature. As a result, specific conductance is a reporting unit that standardizes the conductivity value to 25 oC., thus facilitating comparisons regardless of the water temperature. II. pH pH reflects the acidity or alkalinity of water. The most common pH-related stress is associated with increased acidity or a lowering of the pH of water. pH between 0 – 7 is acidic while a pH between 7 – 14 is basic or alkali.

Most fish have a range of pH values, usually between 6.5 – 8.5, in which they can comfortably live. Aquatic life is usually more tolerant of high pH but not lower pH values. The internal pH of most organisms including humans is between 7 – 7.5. When the external pH of water is much lower, the gills of aquatic organisms can be damaged affecting their ability to extract oxygen from water. Low pH can also change to form of many chemicals and atoms in some cases making them more toxic. Commonly, many toxic metals such as copper, zinc, and iron, are more water soluble at low pH values. Typically significant amounts of copper, for example, are found in water in an insoluble form. However, in the presence of high concentrations of hydrogen ion (the definition of a low pH), copper becomes more water soluble and thus more likely to pose a risk to aquatic life. On the other hand, in a few cases, low pH actually reduces toxicity, such as converting ammonia to its ionized form, which is less toxic.

The measurement of pH can be performed either using pH paper or a pH meter. pH papers are very simple to use, inexpensive, and surprisingly accurate. pH paper strips can identify differences of about 0.2 pH units over a wide range of pHs. A pH meter is the most sensitive way to measure pH and are reliable as long as they are cleaned properly and calibrated frequently. The State Water Board’s Clean Water Team has prepared a series of

fact sheets on the measurement of both conductivity and pH. We encourage you to review them; they are posted at: (http://www.waterboards.ca.gov/nps/cwtguidance.html#40).

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THE STORY OF IRON MOUNTAIN MINES – Acid Mine Drainage Site

Iron Mountain is a 4000 acre mining site off the Sacramento River near Redding where minerals such as copper, iron, and gold were mined starting in the mid 1800s. Nearly 100 years of mining activity produced numerous waste rock and tailings piles and contaminated sediments in nearby waterbodies. The underground mine workings and the fractured bedrock above them provide an effective means for both water and air to reach the sulfide deposits within the mountain, where water and oxygen react with the sulfide ores, producing sulfuric acid and dissolving the heavy metals in the ore. Sulfuric acid is a very strong and toxic acid with an ultra low pH. pH of the effluent from the mine has been measured at a negative pH, specifically -3.8. This makes it the most acidic water ever measured anywhere in the world.

In 2000, microbiologists conducting research inside Iron Mountain announced the discovery of a new species of iron-oxidizing Archaea (along with plants and animals, one of the three primary forms of life on Earth) that thrives in the extreme conditions found in the mine. This organism, Ferroplasma acidarmanus, grows on the surface of exposed pyrite ore in pools of water so acidic that they were previously thought to be inhospitable to all forms of life. It greatly accelerates the rate of oxidative dissolution of pyrite, the process that produces acid mine drainage by converting iron sulfide minerals to sulfuric acid. The discovery of Ferroplasma acidarmanus helps explain why the acid mine drainage problem at Iron Mountain is so severe. According to US EPA, the uncontrolled discharge of copper and zinc from this site is equal to about one-fourth of the entire national discharge of these two metals to surface waters from industrial and municipal sources. This toxic material has damaged parts of the Sacramento River and led to massive fish kills during storms when the toxic soup spilled out of the mine into the river. In one week in 1967, over 45,000 fish were killed by the acid drains. Further, the acid drainage has contributed to the decline in the winter-run Chinook salmon. Source: US EPA Iron Mountain Mine Case Study, posted at: http://www.epa.gov/superfund/programs/aml/tech/imm.pdf.

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2.3. Methods for Measuring Contaminants in Water and Sediment In addition to commonly-measured or conventional water quality parameters, such as temperature and DO, contaminants are a second major class of water quality constituents that you might want to include in your monitoring efforts. Contaminants include metals and organic contaminants, such as pesticides, solvents, and legacy chemicals (e.g. mercury, DDT, and PCBs). Characterizing contaminant concentration in water and sediment can be an important part of a watershed assessment. Frequently, monitoring focuses on measuring contaminants in water, yet many contaminants are organic (fat-loving or lipophilic) and are poorly soluble in water. They tend to stick to particulate matter such as suspended or bedded sediments. If you suspect that a poorly-soluble contaminant might present in your watershed, it is important to test both the water and sediment.. Metals are a class of contaminants often found in the sediment. Most metals are moderately soluble in water, depending on their chemical state. Metals are frequently bound to organic acids associated with debris such as leaf litter or naturally occurring salts. One of the key factors determining the solubility of metals in water is its hardness, the amount of dissolved calcium and magnesium in the water. The greater degree of hardness, the lower the degree of solubility of most metals. The salts actually bind the metals, making them insoluble. Most commonly these bound forms of metals end up sinking to the substrate (i.e., streambed) and cannot be easily absorbed by aquatic organisms from the water. However, they can passed along through the food chain, starting with benthic bacteria, algae, and benthic invertebrates. Thus, determination of water toxicity of metals depends on salinity and hardness, thus salinity and hardness should always been done when testing for measured along with metals so should be tested along with metals. 2.3.1. Overview of Common Classes of Contaminants A brief overview of key classes of contaminants that you might consider including as part of the water quality component of a watershed assessment are reviewed in this section. Information on the sources, toxicity, and fate/transport of the contaminant is summarized for each of the major classes of contaminants. Key to interpreting data on contaminants is information on the reference values, standards, or water quality criteria for the contaminants. 1. Reference Values for Contaminants The US EPA has identified approximately 150 contaminants for which it has set criteria values, which if exceeded in a waterbody could pose a risk to aquatic life. These values are posted at: (http://www.epa.gov/waterscience/criteria/wqcriteria.html). Another useful source of information for reference values is the National Oceanographic and Atmospheric Administration (NOAA) Screening Quick Reference Tables or SQuiRTs (http://response.restoration.noaa.gov/book_shelf/122_squirt_cards.pdf). The list includes a variety of metals such as nickel, chromium, zinc, and copper; solvents such as benzene; hydrocarbons such as anthracene and benzopyrene; and chlorinated hydrocarbons such as DDT. Some of these contaminants can no longer be used in the U.S., however, because they do not degrade easily, they are frequently detected in sediment.

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Criteria values are usually provided for contaminants for both acute (short-term) and chronic (long-term) exposures, as measured by toxicity tests. Acute or short-term toxicity is usually measured by lethality while chronic effects may take longer to appear and are measured as reduced growth rate or impaired reproductive success. In addition to acute and chronic effects commonly measured in toxicity tests, there are many more subtle sub-lethal affects effects of contaminants that are not as easily or commonly measured. Changes in the immune status of a fish or function of key organs are examples of some sub-lethal effects that can be measured using biochemical or molecular methods, not dissimilar to those used by physicians to detect subtle changes in people. The State Water Resources Control Board has posted the CEQA scoping document for the development of sediment quality objectives. The Board has now posted documents used by the Scientific Steering Committee: http://www.waterboards.ca.gov/bptcp/sqoscientific.html#2006. Particularly useful is the March 2006 policy and program overview: http://www.waterboards.ca.gov/bptcp/docs/sqoscientific/2006/march/pres_policy.pdf 2. Pesticides Pesticides are among the most commonly detected contaminants in water and sediment. An excellent source of information on pesticides is the Extension Toxicology Network, a joint project of UC Davis and Oregon State University. The URL is: http://extoxnet.orst.edu/. A brief overview of key classes of pesticides observed in the aquatic environment is reviewed here. a. Chlorinated Pesticides Historically, chlorinated hydrocarbons such as DDT were extensively used to kill agricultural and livestock pests and vectors of human diseases. This class of chemicals exerts its toxicity by disrupting normal nervous system function, either by interfering with peripheral or central neuronal activity, i.e., inhibiting transmission of normal signals along nerves. Chemicals that contain chlorine, such as DDT, tend to be very stable in the environment and bioaccumulate in fat tissues of organisms, including people. DDT was used extensively and is still used today in many other parts of the world to kill mosquitoes which spread malaria. Unfortunately, some of the chlorinated hydrocarbons such as lindane, DDT, and dieldrin, disrupt normal reproductive function in a variety of animals and/or are carcinogens. As a result, most were banned from use in the US in the 1970s and 80s. However, due to their long half-life (the period of time it takes for ½ half of the original amount of the chemical to degrade), which is sometimes over 50 years, traces of these compounds still persist in California water bodies and continue to exert effects in the aquatic environment. For example, DDT or its breakdown products have recently been detected in a number of agricultural drains and sloughs between Fresno and the Delta, likely the result of historic use. These chemicals bioaccumulate, the process whereby a chemical is stored in tissue of an organism and is transferred up the food chain from one animal to another. Many of these chemicals also bioconcentrate, are present in greater and greater concentrations in organisms at each higher link in the food chain.

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Organochlorines have very low solubility in water, so in the aquatic environment, they are found at higher levels in the sediments. Sampling water to test for chlorinated chemicals almost always will result in a negative finding, in spite of the fact that there might be significant quantities associated with the sediment. If your watershed is located in an area where chlorinated hydrocarbon pesticides were once used, traces of organochlorines still might persist in the river bottom or streambed. b. Organophosphate Pesticides Organophosphates (OPs) are a large class of pesticides that were developed as a replacement for chlorinated pesticides because they degrade rapidly, do not tend to bioaccumulate, and are less toxic to humans. However, these pesticides have a higher acute toxicity than many of the organochlorine compounds. Some of the more common OPs are diazinon, malathion, and chlorpyrifos. These pesticides are less toxic to humans, but are highly toxic to aquatic life. Regardless of the specific type of chemical, OPs all act via a common mechanism: the inhibition of an acetyelcholinesterase, an important enzyme involved in nervous system activity. This enzyme is involved in breaking down a neurotransmitter that carries a nervous system signal from one nerve to the next. When the enzyme is inhibited by an organophosphate pesticide, there is excessive nervous system activity, which can eventually lead to loss of neuro-muscular function, paralysis, and death. OPs are more water-soluble than organochlorines. Although the majority of these pesticides found in the aquatic ecosystem are still associated with particles and sediment, a small detectable percentage is dissolved in the water and can be detected in water samples. Similarly to organocholorines, many OPs are currently banned for sale to the general public. They are being phased out of use due to their aquatic toxicity. They are no longer available at hardware and garden stores, but can still be used in agriculture, by pest control specialists, and for other commercial uses. c. Pyrethroids The replacement compounds for OPs are pyrethroid pesticides. They are sold under tradenames such as Capture, Astro, Mavrik, Pounce, in flea powder and collars as permethrin. Since the US EPA banned OPs for retail sales, their use has increased greatly. Today, they are the main pesticide used by consumers. Pyrethroids are all synthetic derivatives of chemicals produced by the flowers of the Chrysanthemum plant. The synthetic versions have been produced since the 1980s and tend to be more stable than the naturally-occurring form. Pyrethroids are also neurotoxicants. They cause toxicity be altering normal sodium and potassium movement into and out of nerve cells. This results in a hyper-excitable state of the nervous system leading to either paralysis or convulsions, depending on the type of pyrethroid, and eventually death. If your budget permits limited monitoring for pesticides, you should give serious consideration to including pyrethroids. Pyrethroids are insoluble in water. They are almost exclusively associated with soil or suspended or bedded sediment due to their very low water-solubility. In general, it is not usually productive to test for pyrethroids in water samples; use sediment samples in their place. These pesticides tend to have short-half lives, on the order of weeks to months, and do not bioaccumulate. However, they are highly toxic to aquatic organisms.

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A reliable source of information for all pesticides is the Pesticide Action Network’s Chemical Database, posted at: http://www.pesticideinfo.org/Search_Chemicals.jsp. This database can be searched in a variety of ways and contains information on all aspects of the chemical. It is particularly helpful because it contains links to peer-reviewed literature, studies that have been screened by a group of qualified scientists. 2. Heavy Metals A second class of chemicals you might want to include as part of a monitoring or assessment effort are metals. The source of metals are both natural and anthropogenic. Unlike pesticides, which don’t support any physiological function, most metals are essential for biological life. All organisms have a window range of required and tolerable concentrations of metals; concentrations outside of this range window may cause problems. Further, metals do not degrade and persist in the environment indefinitely. Some can bioaccumulate in fish tissues. As briefly discussed in CWAM, Vol. 1, Ch. 3.6.5, the solubility of metals in water varies with the hardness (the concentration of calcium magnesium and other positively charged atoms) of the waterbody. In waters with lower levels of hardness, many metals are more soluble, thus more available and increasing the risk for toxicity. Some metals will bioaccumulate in target tissues of an organism, the tissue varying with the specific metal. The current set of US EPA criteria values for aquatic life for many metals are linked to water hardness. A newer approach , known as the Biotic Ligand Model (BLM) is in the process of being adopted that involves assessing toxicity by considering the presence of other water constituents that could bind a metal and prevent it from affecting aquatic organisms. The US EPA promotes the use of the BLM to determine the toxicity of metals. Additional information can be found at: (http://yosemite.epa.gov/water/owrccatalog.nsf/ 0/e693bcf79893c3e085256e23005fcd3b?OpenDocument). This approach involves not only consideration of the solubility of metals, but also their bioavailability and binding to receptors within an organism. Bioavailability reflects that portion of the total concentration of a metal that can enter an aquatic organism; the more bioavailable a metal is, the greater the risk of toxicity Constituents such as organic matter, pH, and temperature of the water as well as the presence of other metals are examples of other constituents in water that could reduce the bioavailability of a metal. The current water quality criteria for metals are based on hardness correction factors, however, over time this newer approach to calculating acceptable levels of metals will evolve to provide a more accurate assessment of risk. The following section reviews key information about metals that are common aquatic contaminants. Additional resources for further data are on the North Carolina State Water Quality Group’s Web site (http://www.water.ncsu.edu/watershedss) or from the Agency for Toxic Substances and Diseases Registry (ATSDR) (http://www.atsdr.cdc.gov/toxfaq.html). Although the ATSDR website has an orientation toward human health, it contains useful information of a general nature. a. Lead Lead is the most widely distributed of the toxic metals. It used to be a component of gasoline, lead shot, insecticides, and paints, and still remains a by-product of smelting in the U.S. It can contaminate water through atmospheric deposition as well as from road-way runoff. Lead is not highly toxic to aquatic organisms, however it can paralyze the

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gizzards of birds, preventing them from properly digesting their food.. In general, lead inhibits oxygen utilization, reduces energy production, and inhibits synthesis of red blood cells. It is estimated that 1 million birds are killed annually due to lead ingestion (Landis & Yu, 2003). The US EPA criteria value, the concentrations of a constituent in water that is safe for most aquatic life, is less than 100 ppb, depending on water hardness. b. Copper Copper is among the most toxic metals in the aquatic environment. It is toxic in very low concentrations. Copper is released into the environment primarily as a result of its uses as a dormant spray in agriculture, as a fungicide in marine paints, and from tailings from copper mines. In urban areas, copper is present in stormwater runoff from roads due to tire wear. Copper is much more soluble in soft water,(less than 75 ppm) than in hard water. It is highly toxic to fish because it disrupts normal electrolyte (salt) balance (Zahner et al., 2006). The US EPA criteria value, the concentration in water that is protective of most aquatic life, is in the low ppb range for most waters; usually less than 20 ppb. c. Mercury Mercury is a heavy metal that is a contaminant throughout California. Sources of mercury include natural release from rocks and soil, mining of mercury, its use in gold mining, and industrial sources, including the burning of fossil fuels and solid waste. In particular, its wide occurrence in northern California is the legacy of the Gold Rush. Mercury contaminates much of in the Sacramento and San Joaquin River systems as well as the Bay-Delta. Mercury is converted by sulfate-reducing bacteria, abundant microorganisms in wetlands, to methyl mercury, a fat-soluble form of the metal. In this form, mercury easily efficiently bioaccumulates and magnifies as it moves up the food chain, from smaller aquatic organisms up to the predatory fish such as bass. It presents a risk to human who consume these fish. Birds that eat fish containing mercury are also at risk of mercury toxicity, including reproductive failure (Schwarzbach et al., 2006; http://soundwaves.usgs.gov/2006/06/). Mercury is a neurotoxin that can cause permanent neurological damage to fetuses and young children. The existing criterion for mercury (measured as total mercury) is 50 ppb. However, its toxicity is primarily associated with its methylated form which bioaccumulates and reach high concentrations in fish tissue. Additional details on the risk of mercury can be found on the Fish Advisory section of the Office of Environmental Health Hazard Assessment’s website: www.oehha.ca.gov/fish.html, Criteria values for fish tissue and methylmercury concentrations in water are under development. CALFED and its partners have devoted considerable efforts to understanding and identifying solutions to the mercury problem in the Bay-Delta. They have produced a report that provides information on its history in northern California, fate and transport, effects on humans, fish, and wildlife, and other relevant topics, which is posted at: http://calwater.ca.gov/Programs/Science/adobe_pdf/MercuryStrategy_FinalReport_1-12-04.pdf.

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d. Zinc Like many of the other metals, small amounts of zinc are essential for life. Too little or too much zinc, copper, selenium, and others essential minerals can cause physiological dysfunction. Zinc is a widespread contaminant in the environment. Environmental sources of zinc include tire wear, and use in a variety of industrial processes, and zinc-oxide roofing material. However, it has a lower level of toxicity than many other metals. The concentration of zinc that is likely to cause harm to most aquatic organisms is on the order of 100 ppb. If fish are exposed to zinc in sufficient concentrations, it can disturb electrolyte balance, interfere with their ability to exchange gases across the gills tissues, leading to hypoxia and death. Like many of the other metals, small amounts of zinc are essential for life. 5. Other metals of concern There are a number of other metals that pose risks to the aquatic environment. To learn about additional metals, you might review the Pesticide Action Network’s Chemical database (http://www.pesticideinfo.org/Search_Chemicals.jsp). Not only does it contain general information and links to peer-reviewed literature on pesticides, but also information on many metals. It is posted at: http://www.pesticideinfo.org/Search_Chemicals.jsp. 2.3.2. Chemical Analysis of Water and Sediment Samples The concentration of certain contaminants (e.g. simazine and atrazine) in water can be measured using relatively inexpensive test kits, if the contaminants is present at sufficiently high concentrations. Test kits can be ordered over the Web and function as good screening tools. Test kits are usually limited to detecting chemicals in the ppm range while many chemicals are toxic in the ppb range – a full 1000-fold lower than what most test kits can detect. Further, test kits are not available for the majority of contaminants of concern. In the majority of cases, however, analytical laboratories are the best place to have water and sediment samples tested for the presence of contaminants. These labs use instruments that commonly measure the concentration of a chemical in the low parts-per-billion (ppb) range, even as low as parts-per-quadrillion. This type of analysis tends to be expensive, potentially costing up to several hundreds of dollars or more per sample. Most of the methods for measuring contaminants generally require expensive and sophisticated instrumentation as well as ultra-clean techniques to avoid introducing contamination into the sample. The California Department of Health Services runs an Environmental Laboratories Accreditation Program evaluates environmental testing laboratories to ensure the high quality work. A list of accredited laboratories is posted at: http:www.dhs.ca.gov/ps/ls/elap/html/lablist.htm. The US EPA publishes standard methods for the analysis of organic contaminants, such as polycyclic aromatic hydrocarbons, phthalates, and other organics of concern. They are posted at: http://www.epa.gov/waterscience/methods/guid/methods.html. In most cases, the laboratory you select can provide appropriate clean containers and a protocol to follow for collecting water or sediment samples. Plastic containers made from high-density polyethylene are typically used for analysis of metals while glass

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containers are most frequently used for the analysis of organic compounds. Most samples should be stored in an ice chest at 4 oC, but not frozen, and a sufficient quantity should be collected to perform all desired tests. Guidance on methods for sample collection has been posted on the website of the State Water Resources Control Board at: http://www.waterboards.ca.gov/nps/cwtguidance.html. This Compendium contains information on field procedures for collection, shipping, and chain-of-custody of water samples. As previously noted, the analysis of sediment samples is sometimes more important than monitoring of water. Many hydrophobic compounds, those with a low solubility in water, stick to fine particles in the streambed sediments and can be detected only in extremely small quantities or not at all in the water column itself. These contaminants could have significant effects on aquatic life either through direct contact with benthic organisms (fish and invertebrates) or indirectly by moving up the food chain. The accurate assessment of contaminants in the sediment depends to a great degree on the accuracy and representativeness of the sample collected. Most frequently, sediment is collected from the top 6” of the streambed. There are a variety of tools and collection methods that can be used for this, from a simple plastic spatula to complex devices for removing sediment cores. The SWRCB’s Clean Water Team has not yet published guidance on sediment sample collection and analysis, however useful information can be found elsewhere. The state of Wisconsin, for example, has a useful website with information on collecting sediment in freshwaters. The Field Procedures Manual is posted at: http://www.dnr.state.wi.us/org/water/wm/sqs/sediment/sampling/701.5.HTM. The U.S. Geological Survey also posts a guide to the collection of bedded sediment samples at: http://ca.water.usgs.gov/pnsp/pest.rep/bs-t.html. The US EPA has published a 3 three-volume series on the assessment of contaminated sediments in freshwater ecosystems (EPA-905-B02-001-B, December, 2002). It contains extensive information on such topics as how to identify sediment quality issues, role of sediment in the aquatic ecosystem, developing a sampling and analysis plan, and methods for assessing whole sediment and pore water. Volume I is posted at: http://www.cerc.cr.usgs.gov/pubs/sedtox/VolumeI.pdf. The other volumes can be easily accessed by editing the URL above for Volume I to read “VolumeII.pdf” and VolumeIII.pdf”. In general, methods for analysis of contaminants in sediment are not as well developed as for water. Consequently, working with a knowledgeable professional is especially helpful when addressing these issues. 2.3.3. Toxicity Testing and Toxicity Identification Evaluations It is often unclear whether the presence of chemical contaminants might be the cause of an observed alteration in the aquatic ecosystem. Toxicity tests are a useful tool to evaluate potential contaminants since they provide general information about the presence of any pollutant. The goal of toxicity tests is to determine if any constituent in a water or sediment sample might cause harm. Toxicity tests are performed in a laboratory using defined test conditions. These tests typically measure mortality or effects on growth and reproduction in a variety of invertebrate and vertebrate test organisms such as a water flea or fathead minnow. The limitation of these tests is that they usually do not detect subtle effects such as changes in physiological processes that are often the precursor to more overt and serious consequences.

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There are standard plant and animal test organisms for various types of toxicity tests. Acute and chronic tests can be run for anywhere from 48 hours to a month. The organisms are usually placed in a beaker or small fish tank containing water or sediments collected from the waterway of interest. The organisms are maintained under controlled conditions so that parameters such as DO and temperature remain constant, thereby limiting the effects of extraneous factors. If mortality is the endpoint of interest, the number of dead organisms at the end of the exposure period is compared to the control group. If effects on reproduction are being evaluated, the number of offspring in organisms exposed to the suspect sample are counted and compared to a control group. Reproduction, growth, and mortality are the most commonly measured parameters. Toxicity tests are conducted at specialized laboratories. They must follow carefully defined guidelines prescribed by the US EPA. A review of the numerous types of freshwater and marine toxicity tests, including their strengths and weaknesses, is posted at: http://www.oehha.ca.gov/ecotox/pdf/marinetox3/pdf. If toxicity is identified in the water or sediment sample, the next step is to determine what constituent(s) are responsible for the observed effects. Using toxicity identification evaluations (TIEs), a positive identification is frequently possible. There are 3 basic phases of this process.

• Phase I involves identification of the general chemical groups of the toxicant(s). This is accomplished by physically or chemically manipulating the sample to remove or alter specific groups of chemicals.

• Phase II isolates the causative toxicant and makes a tentative identification. • Phase III confirms the causative toxicants using sensitive analytical instruments

or biochemical methods of analysis. The combination of toxicity tests and TIEs are extremely useful methods identifying chemical stressors in a waterway. While most TIEs are performed on water, some newer methods have been developed to identify toxicity in sediments as well. 2.4 Analyzing the Data 2.4.1. Identifying criteria values or reference conditions Water quality data is an important part of any watershed assessment. It plays an important role in evaluating the overall health of a watershed. Comparing conditions in your waterway to those known to protect aquatic life as well as serve human uses is an important factor in characterizing the conditions of your watershed. This analysis involves a) comparing your findings to criteria values, and b) using this comparison as a basis for evaluating the conditions in your waterways. Comparing your data to established criteria or literature values In the first section of this chapter, we briefly discussed the importance of comparing your data to recognized values from either the US EPA, the scientific literature, or nearby reference waterways. The importance of this step cannot be overemphasized. This

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comparison is the basis for determining if the water or sediment quality is appropriate to support aquatic life or meet other needs and goals for the waterway. For example, if the temperature of the water is consistently higher than that which will support reproduction of cold-water fishes, then this will be an important issue you will want to address in your final analysis as well as include in a management plan. There are a number of source of information on protective values for aquatic life:

• US EPA Ambient Water Quality Criteria. These are concentrations of conventional water quality parameters as well as contaminants that have been calculated to be protective of most aquatic life. They are periodically revised and expanded to cover more parameters. They are available online at: http://www.epa.gov/waterscience/criteria/wqcriteria.html.

• Regional Water Quality Control Board’s Basin Plan. These plans contain a section with numeric or narrative water quality objectives for local waterways. These values are usually the same or very similar to EPA criteria.

• Sediment Quality Objectives. • Scientific literature. Peer-reviewed scientific literature contains research results

indicating pollutant levels likely to pose a risk to aquatic life or human health. Google Scholar (http://www.scholar.google.com) is one way to search for scientific literature. University libraries have many databases that are easily searchable. For data on aquatic life, the Aquatic Sciences and Fisheries Abstracts (ASFA) is an excellent database that contains scientific reports on a wide variety of water quality characteristics important for maintaining aquatic health. Most common are laboratory studies performed under controlled conditions. In some cases, the results can be applied directly to field conditions. But it is advised to consult with a fisheries biologist or toxicologist to review the data and determine how you might be able to utilize the information.

• Surrogate Water Body Reference Values. Many times the best way to gauge the conditions in your local waterway is by comparing it with a more pristine stream in the same ecoregion. But there are few pristine or untouched water bodies remaining in California today. However, on a relative scale, there are some watersheds that have maintained relatively good structure and function. Reference values, as used here, are concentrations in water or sediment that represent the best regional conditions. Information on reference values from regional waterways are especially useful because they reflect a variety of field conditions which frequently cannot be duplicated in laboratory studies.

One consideration to keep in mind once you have completed the comparisons is the effect of multiple exceedances; the effects can be additive or synergistic. In other words, the occurrence in a waterway of several minor water quality problems may add up to major effects on aquatic organisms. For example, if salmonids are already slightly stressed by elevated temperatures (that are not fatal and support reproduction), then the influx of pesticides from a first-flush storm may cause sickness or mortality that fish in colder water might have survived. There are many scientific studies that have addressed the issue of multiple stressors and their possible additive and/or synergistic effects. Following the approach used in human health risk assessment and in the absence of evidence to the contrary, when many pollutants occur together, you can assume that their effects on aquatic organisms are additive. This is especially true if the different contaminants work via the same mechanism. For example, if three pyrethroid pesticides

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are each present in a water sample, it is reasonable to assume that their effects will be additive. Research on the effects of the Exxon Valdez oil spill showed that the polycyclic aromatic hydrocarbons in the oil depressed the immune system of many fish. When they were exposed to bacterial challenges instead of being able to fend off the infection, many succumbed to its effects. The challenge is that there are so many possible combinations of chemical, biological, and physical stressors that it is nearly impossible to study and understand all the possible consequences. 2.4.2. Descriptive Statistics The way in which you represent data graphically can serve as an aid to interpreting its meaning. To illustrate some of the options, assume a watershed group has collected data on water quality for a local stream. Copper concentrations in the water ranged from 6 to 20 parts per billion (ppb). Samples were collected from 7 sites. First, the criteria value for the protection of aquatic life was identified in the US EPA Ambient Water Quality Criteria list (AWQC; http://www.epa.gov/waterscience/criteria/wqcriteria.html). Two sets of values exist: those for chronic or longer-term exposure and those for acute or short-term exposure. Since this waterway is near a freeway, there is a continual source of copper wearing off of tires that introduces the contaminant into the watershed via stormwater runoff and air deposition. The group decided to select the chronic value for comparison. Since the AWQC value is dependent on the hardness of water, the group used a correction factor to determine the actual criteria value for their waterway. They determined that the corrected AWQC value was 8 ppb. The Hazard Quotient, ratio of the measured copper concentration and the criteria value, was calculated to determine potential impacts to aquatic organisms. The data was assembled in a table as follows:

Sampling Site Mean copper concentration

(ppb; quarterly samples) Ratio between measured

and criteria value

SS 1 12 15/8 = 1.875 SS 2 15 12/8 = 1.5 SS 3 18 10/8 = 1.25 SS 4 20 20/8 = 2.5 SS 5 7 7/8 = 0,875 SS 6 6 6/8 = 0.75 SS 7 6 6/8 = 0.75

The following 2 graphs could be constructed from the above data.

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MEAN COPPER LEVELS IN POKER CREEK

02468

1012141618

Cu conc.

part

s pe

r bill

ion

(ppb

) Figure 1. The relationship between the

average concentration of copper in “Poker Creek” compared to the criteria value (red line). The variation in the data is reflected by the standard error bar. This type of graph tells a simple story – on average, copper in the water of this stream exceeds a safe concentration for aquatic life.

Copper concentrations in Poker Creek

05

1015202530

SS1 SS2 SS3 SS4 SS5 SS6 SS7sampling site

ppb

Figure 2. Copper concentration at different sampling locations. Bars represent the mean plus standard error for 4 monitoring dates in 2005 for copper at all the different sampling sites, from SS1 near the bottom of the watershed to SS7 at the top. It shows that 4 out of 7 of the sites sampled exceed the criteria value, or a 58% exceedance rate. It also suggests a spatial distribution of values. The lower reaches of the stream (SS1 – SS4) have higher concentrations, suggestive of copper-containing effluent between SS4 and SS5.

If data had been collected over a number of years, additional information could be illustrated in the graphs. Further, if toxicity data was available, it could be compared to the copper concentrations, as follows:

0

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SS 1 SS 2 SS 3 SS 4 SS 5 SS 6 SS 7

Sampling Site

ppb

copp

er

0102030405060708090100

perc

ent m

orta

lity

Cu conc.% mortality

Figure 3. Copper concentrations and percent mortality at various sites in Poker Creek. Bar represents the mean of samples collected over 3 years; line reflects the average mortality for water fleas, Ceriodaphnia dubia.

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In Figure 3, the toxicity data, reported as percent mortality, is represented by the blue line. The purple bars are the copper concentrations at various sites in the stream. The fact that both variables track each other quite well is an indication that they are linked; that the high copper concentrations, at levels that exceed safe values for aquatic life, might be responsible for the mortality. However, it is also possible that another more toxic contaminant that is associated with the copper could be causing the toxicity. The presence of a correlation does not always mean cause and effect relationship exists. In summary, tables, graphs, and figures that represent descriptive statistics are a good starting point for understanding watershed data It serves as an aid to interpreting what the data means and the implications for the assessing and future management plan. 2.4.2. Formal Statistical Analyses An important part of the analyses in a watershed assessment is to determine if there is a relationship between physical, chemical, and/or biological aquatic parameters you measure and influential processes in the watershed. Water quality measurements are often made to study potential effects of diffuse sources of pollution on aquatic ecosystems and drinking water quality. This section will review how to use formal statistical analyses to better understand these relationships. In addition, CWAM Volume I, chapter 5 and CWAM Volume II, chapter 1, provide introductions to data analysis, including an introduction to correlation analysis. 1. Evaluating the relationship between water quality data and aquatic life

0

20

40

60

80

100

0 5 10 15 20 25Cu concentration

% m

orta

lity

Many of the water quality parameters described in this chapter can impact aquatic organisms and cause physiological stress, reproductive problems, or death. Absence of organisms from a waterway could indicate that it is not suitable habitat, or that some condition in the watershed prevents aquatic life from surviving. If habitat conditions are suitable and the organism is present in similar streams elsewhere, then a water quality impact may be responsible for its absence. Similarly, if the composition of aquatic communities (e.g., benthic macroinvertebrate or periphyton assemblages) is different among similar reaches, then water quality problems may be one of the explanatory or driving variables. If you have both aquatic community data and water quality data in hand sufficient to evaluate conditions of reaches, waterways, and/or sub-watersheds, then you may be able to statistically explain variation in the aquatic community data using the water quality data.

Figure 4. The effect of copper in water on mortality in fish. The lines indicates the regression relationship between the independent variable, copper, and the dependent variable, mortality. As copper concentrations increased, mortality increased in a linear fashion.

The process for comparing water quality data to

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biological data starts with identifying a potential mechanism or process by which changes in water quality can influence aquatic organisms and communities. This is similar to the conceptual modeling process described in CWAM Volume I, Chapter 2. Once you have developed this conceptual or linkage model, you have a way to structure your statistical analysis. The core idea you will probably work with is that some measured change in water quality caused a measured change in aquatic communities. The simplest explanation is that a single water quality variable is responsible for a single or small set of effects. A valuable way of analyzing water quality data is to note changes over time, especially if restoration efforts are ongoing or if new policies have been enacted. Tracking changes over time can provide insight into the effectiveness of the new measures. These trends lie at the heart of adaptive management, i.e., evaluating the effectiveness of actions in the watershed and subsequent adjustments in the policies or practices, as needed. Trends analysis can also be used to develop a watershed indicator report. The following example suggests a simple way to begin to identify if changes are occurring over time. 2. Simplified Trends Analysis In the following hypothetical example, a watershed group collected temperature data using data loggers every 15 minutes for about 3 years. The questions they have are a) has there been an increase in the temperature over that period of time and b) does the average temperature exceed that which is protective of aquatic life. It is generally difficult to detect a change in temperature over time because it is not easy to distinguish between natural variability and a trend that reflects real change. Complex statistical methods have been develop, known collectively as trends analysis or time series analyses, to address this issue. However, there are some simpler approaches that can be used to gain a first approximation of the trends. These simpler methods will be reviewed. Using the temperature example, the data can be broken down into seasons and simple comparisons of temperature trends for the same season for 3 consecutive years can be made. In the Poker Creek example, fall run Chinook salmon use the creek for spawning

Water quality impacts from grazing Scientists in Canada have compared effects of cattle grazing on water quality in side-by-side small watersheds (Mapfumo et al., 2002). Over a 3-year period, they found that increases in runoff volume, total dissolved solids, electrical conductivity, and nitrates correlated with grazing intensity. They used canonical correlation analysis to compare potential sources of water quality degradation (e.g., weather, grazing management) with water quality constituents (e.g., nutrients, organic carbon). This approach delivers the best “fit” between observed effects and potential influences (e.g., management conditions). Canonical correlations are used similarly to simple correlations, however instead of comparing one variable to another, canonical analysis supports the comparison of set of variable to another set of variables, as in the example above. The analysis lets the user see how each variable in each set uniquely contributes to the respective weighted sum .

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in late fall so the watershed assessment team decided to break the seasons into 3 groups corresponding to the needs of the fish: fall temperatures which are defined by the needs of spawning fish; winter-spring temperatures which are defined by the needs of alevins and juvenile salmon, and summer-early fall, a time of year in which salmon generally aren’t present. The assessment team retrieved standards from their Regional Water Quality Control Board’s Basin Plan to gain an understanding of the desirable temperatures during the seasons with which they were concerned. Three sets of graphs were prepared representing each season; below are those for the winter-spring temperatures. Two key factors stand out in the results. First, there are exceedances of the water quality standard for temperature in the late spring. Second, the slope of the trend line seems to be shallower over consecutive years.

Poker Creek Spring 2004 Temperature Temperature Ob jectives

Temp °C = -3929.9695+0.1036* x

12/25/03 1/14/04 2/3/04 2/23/04 3/14/04 4/3/04 4/23/04 5/13/044

6

8

10

12

14

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18

20

22

24

26

Tem

p °C

DatePoker Creek Spring 2005 Temperature

Temperature ObjectivesTemp °C = -2883.6108+0.0754*x

12/19/04 1/8/05 1/28/05 2/17/05 3/9/05 3/29/05 4/18/05 5/8/05

Date

4

6

8

10

12

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Tem

p °C

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Poker Creek Spring 2006 Temperature Temperature Objectives

Temp °C = -2557.2623+0.0662*x

The red horizontal lines in each graph represent the water quality objectives for temperature for different months of the year as identified in the Basin Plan. A simple regression analysis was performed to estimate the slope of the line for all the data for each year. The slopes were 0.103, 0.075, and 0.066 for 2004, 2005, and 2006 respectively. These correspond to the fewer number of days in which springtime water

12/14/05 1/3/06 1/23/06 2/12/06 3/4/06 3/24/06 4/13/06 5/3/06 5/23/064

6

8

10

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14

16

18

20

22

24

26Te

mp

°C

Date

Poker Creek Temperatures Spring 2004-2006

2004: y = 0.1073x - 4187.1R2 = 0.8029

2006: y = 0.0658x - 2563R2 = 0.613

2005: y = 0.0765x - 2981.2R2 = 0.8218

0.00

5.00

10.00

15.00

20.00

25.00

1/1 1/8 1/15

1/22

1/29 2/5 2/1

22/1

92/2

6 3/5 3/12

3/19

3/26 4/2 4/9 4/1

64/2

3

200420052006Regression 2004Regression 2006Regression 2005

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temperatures exceeded the water quality criteria. Although the total amount of time the temperature exceeded criteria values decreased with each consecutive year, for at least 2 weeks each year the temperature exceeded that which is known to be safe for juvenile salmon. By comparing the slopes to each other, an initial estimate can be made if there is a trend of decreasing spring temperature over the 3 year period. Factors that might influence this trend, such as air temperature, precipitation, or amount of imported water (if applicable), should be analyzed to identify possible influences on the temperature. It might be worthwhile to develop a specific conceptual model for temperature, the stressors that might cause changes, and the possible sources of these stressors. It can serve as guide for what additional information you will need to identify the source of the temperature exceedances. To gain an understanding if there is a trend for increasing or decreasing temperature, a few estimates can be made. The above figure illustrates the daily averages for springtime water temperatures for 3 consecutive years. The figure was created in Excel using a line plot. A trend line was inserted to estimate the differences in temperature during the time of year when alevin and juvenile salmon are in the creek. As noted earlier, it appears that the slope of the temperature regression lines decrease over consecutive years. To estimate if this difference might be significant, 95% confidence intervals were constructed around each of the regression lines using a statistics software program.

Poker Creek Spring Temperatures

4

6

8

10

12

14

16

18

20

22

2004 temp 2005 temp 2006 temp1/1 1/11 1/21 1/31 2/10 2/20 3/2 3/12 3/22 4/1 4/11 4/21

Date:2004 temp: y = 6.3842 + 0.1073*x Date:2005 temp: y = 7.9369 + 0.0765*x Date:2006 temp: y = 8.2715 + 0.0658*x

Date

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The 2004 (red line, square markers) confidence intervals do not overlap with either the 2005 (black line, triangle markers) or 2006 (blue line, circular markers), except where they cross over each other. In contrast, the 2005 and 2006 confidence intervals overlap with each other in mid February. This suggests that a there might be a significant difference between 2004 and 2005/06 temperatures. While this estimate can be used to estimate real differences, it can also suggest there are no differences between years when some exist. The significance level of 95% is commonly used but there is no reason that a 90% confidence level might be just as valid. This level of confidence would suggest that there is a 9 out of 10 chance that 2004 temperatures are higher than subsequent years; a pretty high level of confidence. These caveats suggest that graphical method for estimating differences are useful, especially when assessment budgets are limited. For greater insight, a more complex trends analysis should be performed. 3. Summary of Water Quality Analysis Considerations The following are general steps you might used as a guide when analyzing water quality data: 1) Choose the factors you are interested in comparing. It could be peak temperature over many years or daily/weekly average pollutant concentration. While comparisons of various water quality parameters over time is one approach, investigating relationships between these parameters and other biological endpoints, such as fish populations or data on benthic macroinvertebrates, provides insight into the effects of water quality parameters on aquatic life. 2) Prepare a series of simple graphs, such as those illustrated above, to display the data. This is the first step in gaining an understanding of the potential relationships that might exist. Spatial or temporal relationships may become apparent. Relationships between water quality characteristics and biological life may be reflected in the graph. 3) If you observe what appear to be important relationships, perform statistical analyses. Determine what type of statistical test you should use based on your question. If you are comparing a water quality parameter with a biological measurement, you can consider using correlation or regression analysis and test for the significance of the slope. Use analysis of variance to compare different sub-watersheds. Analysis of variance can be used if your data is normally distributed. If not, Chi Square analysis or other non-parametric statistics is an alternative. Trend or time series analysis is useful to determine if there are significant changes over time. 4. Correlations vs. cause-and-effect Recognizing the difference between a correlation and a cause and effect relationship is important to appropriately interpret watershed data. Correlation is the simultaneous change of two numerical variables, such as increased water temperature with decreased canopy cover (negative correlation) or an increase in water temperature with an increase in the volume of wastewater treatment effluent (positive correlation). Correlation coefficients can be calculated in Excel or with statistical software. They reflect the strength of the correlation, i.e., how positively or negatively two factors are related to each other.

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However, correlation does not necessarily mean that one factor caused the other although in some cases this may be true. It simply means that two factors vary at the same time; a third independent factor could be responsible for the variation in both. Cause and effect is more difficult to identify than correlations. There is no single statistical test that can determine if a cause-and-effect relationship exists. However, there are systematic approaches to sorting out if a cause-and-effect relationship exists. One such approach has been developed for identifying biological impairments has been described by the US EPA; the Stressor Identification Process. This approach helps managers identify the possible causes of impairment by using a systematic process of inductive reasoning. This guidance describes a set of criteria, based on those used in human epidemiology, which can be used to evaluate the nature of a possible cause-and-effect relationship:

• Can a complete causal pathway be identified? If fish are dying, is there a way to explain how temperature might have caused this to occur.

• Does the stressor occur at the same time as the impairment? Also known as temporal co-occurrence. The stressor (e.g., high temperature) and the impairment (death of fish or disappearance of fish) should occur at about the same time;

• Does the influence and the effect occur in the same geographical area (spatial co-occurrence);

• Has a dose-response relationship between the possible cause and effect been established? For example, at higher and higher temperatures, do fish show signs of distress? This kind of information would be found in scientific articles.

• Is there a gradient? As you move farther and farther away from the high water temperature, does the effect becomes increasingly smaller? If this was the case, it would suggest that high temperature is the factor causing effect.

If all or most of these criteria are met, it is likely that a cause-and-effect relationship exists. If not, however, it is unlikely that one factor cause the response you have observed, even if a positive correlation exists between the factors. In this case, a third, unidentified factor could be responsible for the changes you have observed. There are additional criteria that can be used to help strengthen the relationship between water quality and other watershed parameters. These are reviewed on the US EPA website: www.epa.gov/caddis. 2.4.3. Using Geographical Information Systems to Understand Spatial Relationships A complementary approach to traditional statistical analysis is to use spatial analysis and statistics using a GIS. Frequently, the most interesting issues in a watershed assessment relate to differences between sub-watersheds or identifying the contribution of certain upland activities to in-stream conditions (Richards et al., 1996). In many cases, landscape contributions to water quality are not considered when locations are selected for monitoring stations. However, with some creativity you can still measure or get some indication of the landscape influence. One way to do this is to use GIS to isolate that part of the landscape, and thus those features and activities that are hydrologically linked to the site, typically areas which are upstream and uphill of the monitoring station. Because there may be several monitoring stations along a waterway,

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the upstream ones will be nested within the watershed area contributing to conditions at the lower stations. This will allow you to evaluate differences along the waterway and infer contributions from the watershed area between the stations. In some cases, specific pollutants or conditions may suddenly appear due to some activity in the watershed at a particular location. In other cases, water quality may steadily worsen as you go downstream because of continuous inputs from the landscape (e.g., fine sediments from roads) or in-stream processes (e.g., algal growth from nutrient inputs). Depending on the contours of the land, everything upstream of a sampling site doesn’t necessarily contribute to a water quality conditions at a certain location. In some cases, drainage patterns may be irregular. To understand these potentially irregularities, using a hydrological modeling tool with a GIS can help more accurately delineate landscape inputs at a certain point along a waterway. Another useful way in which GIS can help you interpret water quality data is by analyzing the areal extent (acreage) and location of different land uses in each sub-watershed. The underlying assumption here is that different land uses are associated with different types of influences on water quality as well as other type of aquatic conditions and processes. By identifying land use types, industrial sites, the location of wastewater treatment plants, the amount of imperviousness, and a variety of other factors in a GIS, you can begin to gain an understanding of the potential inputs that could affect water quality. The Relative Risk Model (RRM) (Wiegers et al., 1998) is based on the premise that the areal extent of different land uses typically associated with the release of pollutants are positively correlated with water quality. Therefore a greater risk for poor water quality exists when industrial or urban land uses predominate in a

Analysis of nutrients with a GIS: an example Spatially-explicit models have been developed that simulate production of pollutants (e.g., nitrogen-containing compounds) from different land uses and cover. Two of these are the “DRAINMOD” family of models and “WATGIS” (which uses certain DRAINMOD components). Geographic data showing the distributions of natural features (e.g., soils and waterways) and human uses (e.g., agriculture type) are combined with precipitation and other information to simulate the production of nutrients within the watershed to the waterway. The model developers have tested and validated the model outputs using field-collected data. DRAINMOD (www.bae.ncsu.edu/soil_water/drainmod.htm) WATGIS (Fernandez et al., 2002) www.srs.fs.usda.gov/pubs/7130) SNTEMP (www.fort.usgs.gov/Products/Software/ SNTEMP) SWAT (www.brc.tamus.edu/swat/soft_model.html)

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watershed than if there was less intensive use. This approach assumes that risk can be estimate from quantifying the areal extent of the different land uses, the extent of habitat, and a number of other related factors. The RRM is designed to estimate risk posed by sources of stressors (land uses, human activities) to aquatic life and other aquatic resources, including water quality. More details of this model were discussed in CWAM, Vol. I, Ch. 6. A PowerPoint presentation by Professor Landis, the developer of the RRM, is posted online at: http://www7.nationalacademies.org/sustainabilityroundtable/WLandis_Presentation.pdf and provides a helpful introduction to the RRM. A significant number of peer-reviewed articles on the topic are also available at most university libraries. 2.5 Conclusions This chapter has reviewed key issues and basic techniques involved in water quality monitoring as a key part of a watershed assessment. In summary, the following steps should be considered when collecting water quality data as part of a watershed assessment:

1. Gather and assess existing information Assessing the amount and type of existing data will help save time and focus future efforts on filling data gaps.

2. Select parameters and constituents for monitoring Determine which parameters you are interested in measuring. Almost all monitoring programs include commonly-measured parameters such as DO, temperature, and pH. Consider if collecting sediment instead of water samples might be more appropriate media in light of the constituents you are interested in monitoring. 3. Design the sampling plan To design the most appropriate sampling plan, consider the purpose of the effort. If you are interested in detecting “hot spots”, collect samples upstream and downstream from the sites of concern. If you are interested in getting an overall picture of the watershed, use a random sample design. If you are interested in learning about conditions in each of the tributaries of your watershed, use a stratified random sample design. Consider daily or seasonal variability of the parameters you are measuring. Sample as frequently as needed to obtain an accurate picture of the condition you are evaluating. 4. Collect samples following standard methods In order to obtain the most accurate analysis of sediment or water samples, be sure to use appropriate collection techniques. The place in the water column or streambed from which you collect your sample, and how the sample is handled will affect the accuracy of the analysis. 5. Use appropriate analytical methods. Select a certified analytical lab to perform any analyses you are unable to do yourself.

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6. Compare your results with reference values Once the analyses of the samples has been completed, compare the data with reference values, such as ambient water quality criteria, reference values from less impacted waterways in your region, or values from the scientific literature. This will help you evaluate the meaning of your data; for example, does it protect aquatic life. 7. Summarize the results graphically Preparing graphs of your findings is usually the easiest way to begin to understand the data and possible relationships or trends. The figures you prepare can also be used in your watershed assessment or other reports. 8. Perform statistical analysis when possible If you have only a small amount of data collected over a limited period of time, simple descriptive statistics (means and a measure of variability such as standard deviation) might be the best place to start. If possible, however, a statistical analysis, such as linear regression, Chi square, or trends analysis should be performed if warranted. 9. Place your findings in the context of the landscape In the final analysis, placing your findings in the context of the watershed will help you to gain insight into the relationships between land uses and/or discharges and the conditions in the waterway. Use a conceptual model (see Chapter 1) or similar approach to illustrate conclusions about possible connections between watershed and sub-watershed conditions and uses. Describe or show analytically how water quality problems are correlated with aquatic habitat issues. Identifying these important relationships is an important part of data integration and supports the development of a watershed management plan.

Acknowledgements Special thanks to Karen Randles and Ashley Cates, OEHHA, for editing this chapter. Appreciation is extended to Randy Grose, David Ford Consulting, for advice on the statistical section of the chapter. 2.6 References Boyd, M. and B. Kasper. 2004. Analytical methods for dynamic open channel heat and mass transfer: methodology for the Heat Source model version 7.0. http://www.heatsource.info/Heat_Source_v_7.0.pdf Drost, C.A. and G.M. Fellers. 1996. Collapse of a regional frog fauna in the Yosemite area of the California Sierra Nevada, USA. Conservation Biology, 10:414-425. Fernandez, G.P., G.M. Chescheir, R.W. Skaggs, D.M. Amatya. 2002. WATGIS: A GIS-based lumped parameter water quality model. Transactions of the ASAE. 45(3): 593_600.

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Hitt, N.P. 2003. Immediate effects of wildfire on stream temperature. Journal of Freshwater Ecology. 18(1): 171. Le Noir, J.S., L.L. McConnell, G.M. Fellers, and T.M. Cahill. 1999. Summertime transport of current use pesticides in the Sierra Nevada Mountain Range, California, USA. Environmental Toxicology and Chemistry. 17: 1908-1916. Mapfumo, E., W.D. Willms, and D.S. Chanasyk. 2002. Water quality of surface runoff from grazed fescue grassland watershed in Alberta. Water Quality Research Journal of Canada. 37(3): 543-562. Richards, C., L.B. Johnson, and G.E. Host. 1996. Landscape-scale influences on stream habitats and biota. Can. J. Fish Aquat. Sci. 53 (Suppl. 1): 295-311. Schwarzbach, S.E., Albertson, J.D., and Thomas, C.M., 2006, Effects of predation, flooding, and contamination on the reproductive success of California Clapper Rails (Rallus longirostris obsoletus) in San Francisco Bay: Auk, v. 123, no. 1, p. 45–60. Sparling, D.W., G.M. Fellers, and L.L. McConnell. 2001. Pesticides and amphibian population declines in California, USA. Environmental Toxicology and Chemistry. 20(7): 1591-1595. Torgersen, C. E., D. M. Price, H. W. Li, and B. A. McIntosh. 1999. Multiscale thermal refugia and stream habitat associations of chinook salmon in northeastern Oregon. Ecological Applications 9: 301-319. Torgersen, C.E., R. Faux, B.A. McIntosh, N. Poage, and D.J. Norton. 2001. Airborne thermal remote sensing for water temperature assessment in rivers and streams. Remote Sensing of Environment 76(3): 386-398. US EPA, 2001. Summary of Technical Literature Examiniing the Phsyiological Effects of Temperature on Salmonids, Issue Paper 5, EPA-910-D-01-005, US EPA, Washington, DC. Welsh, H.H., Hodgson, G.R., Harvey, B.C., and Roche, M.F. 2001. Distribution of juvenile coho salmon in relation to water temperatures in tributaries of the Mattole River, California. North American Journal of Fisheries Management. 21(3): 464-470. Wiegers, J.K., H.M. Feder, L.S. Mortensen, D.G. Shaw, V.J. Wilson, and W.G. Landis. 1998. A Regional Multilpe-Stressor Rank-Based Ecological Risk Assessment for the Fjord of Port Valdez, Alaska. Human Ecol. Risk Assmt. 4: 1125-1173.

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APPENDIX I. Reporting temperature measurements The simplest way to report temperatures is through graphs and tables. There are also several temperature metrics that can be calculated and used to assess conditions in your watershed, especially as they relate to aquatic life. These are most meaningful when they are accompanied by a description of how the metric values relate to habitat quality. 1. Daily maximum/minimum temperature has been used to compare streams that have different exposure to disturbance. In one example, the maximum daily temperature for a stream after a severe fire was higher than the maximum daily temperatures for a stream in an unburned area (Hitt, 2003). The minimum daily temperatures were no different. The combined findings for minimum and maximum daily temperatures suggest that the streams were basically similar, but that the disturbance from fire resulted in daily elevation of water temperature (likely due to lack of tree cover). 2. Maximum Weekly Maximum Temperature (MWMT) is the highest mean of maximum daily temperatures over 7-day periods. To calculate this metric, you would identify the highest temperature at a monitoring point for each day of 7 days in a row. You would then calculate the mean maximum temperature for that 7-day period. The MWMT represents the highest value of these 7-day periods. This is a sensitive indicator of potentially damaging temperatures in streams. This metric has been used to study land-use effects on juvenile salmon distributions and a correlation was found between MWMT and distributions (Welsh et al., 2001). 3. Maximum Weekly Average Temperature (MWAT) is related to MWMT except that instead of using the maximum daily temperatures, you calculate the mean daily temperatures for each day of a 7-day period, then calculate the (weekly) mean of these mean daily temperatures. The highest of these weekly means is the MWAT. It is typically higher than the optimal temperature that supports normal physiological functions. This indicator is less sensitive than MWMT of potentially damaging temperatures in streams. This metric has been used to study land-use effects on juvenile salmon distributions and a correlation was found between MWAT and distributions (Welsh et al., 2001). 4. Daily temperature cycles are the range of temperatures which waterways experience during a given day (Figure 1). These cycles will have the greatest range in the following conditions: removal of vegetation through fire or logging, low flows due to natural or water management conditions, large difference between night-time and day-time air temperatures. The greater the range of temperatures, the more likely certain species will not grow, thrive, or survive in a waterway.==> make this one #1 and calculate others using the same dataset 5. Maximum or lethal temperature is the temperature that will kill aquatic life over some defined time period (e.g., 1 hour). The temperature will vary by species and life stage and the time period chosen. Different terms are used to refer to this concept, including terms that are defined by half (vs. all) of the affected individuals dying, or are defined by

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e C

)

Figure 1. Daily fluctuations in water temperature (data courtesy Friends of Deer Creek for Deer Creek site 22, just upstream of Nevada City).

populations or species suffering chronic problems (e.g., disease) because they are weakened by elevated temperatures. II. Temperature Modeling One potential use of temperature monitoring data is to model temperature in a waterway under existing or alternative future conditions. Temperature modeling requires information about several basic watersheds characteristics – tributary water temperature and flow rate, local climate, land cover, and surrounding land-forms. These characteristics are a combination of the water sources and factors that influence temperature in the modeled reach. Groundwater temperature and influx into surface waterways can also affect surface water temperature, but is harder to measure and is usually inferred from measuring changes in surface water temperature along a waterway. Most temperature models estimate heat transfer between major compartments (e.g., surface water and ground water, surface water and air). They can also estimate actual water temperatures based on parameter inputs and calibration you provide. The reason that this may be important is that water temperature can be highly variable within waterways and between seemingly similar waterways

Stream Network Temperature Model (US Geological Survey) This model was developed to provide a way to simulate daily mean and maximum stream temperatures based on heat inputs from the surrounding environment. Input parameters include riparian cover, solar radiation, evaporation and convection, groundwater inputs, and other factors. The model results can be validated using newly-collected data, or archived data. This model has been used to study the impacts on water temperature of riparian shading, reservoir storage and releases, and water diversion. http://smig.usgs.gov/cgi-bin/SMIC/model_home_pages/model_home?selection=sntemp

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(Boyd and Kasper, 2004; Torgersen et al., 1999 & 2001). Although a temperature model may be very useful to your study, it can be only as good as the data used to calibrate it and to simulate alternatives. You may be able to run a model for your waterways if you have adequate information about land cover (e.g., actual height and extent of riparian forest), locations and in-stream flows of streams and creeks, climate (e.g., air temperature), and water temperatures during daily and annual cycles at several places along a waterway. Lacking any of these may make the model outputs of water temperature less meaningful. III. Water Temperature Thresholds and Standards Since salmon are the focus of consideration in many watershed protection and habitat restoration efforts, the following table, provided by Calfire, may be helpful to those watersheds that serve as salmon habitat.

Mean Weekly Average Temperature Thresholds and Standards for Salmon Temperature ( C ) Descriptions Temperature (F)

26 Upper end of range of acute thresholds (considered lethal to salmonids)

78.8

25 77.0 24 Lower end of range of acute thresholds

(considered lethal to salmonids) 75.2

23 73.4 22 71.6 21 69.8 20 68.0 19 Steelhead growth reduced 20% from maximum

(Sullivan and others, 2000).MWAT metric USEPA (1977) growth MWAT for rainbow trout Coho growth reduced 20% from maximum (Sullivan and others, 2000), MWAT metric

66.2

18 USEPA (1977) growth MWAT for coho 64.4 17 Steelhead growth reduced 10% from maximum. 62.6

16.8 NMFS MWAT threshold. 62.2 16.7 Welsh and others (2001) MWAT threshold for coho

presence/absence in the Mattole 62.1

16 Oregon Dept. of Environmental Quality Standard for salmonids (equivalent MWAT calculated from 7-day max.)

60.8

15 EPA Region 10 Recommended MWAT. Threshold for Coldwater Salmonid Rearing

59.0

14.8 Coho growth reduced 10% from maximum (Sullivan and others, 2000), MWAT metric

58.6

14.6 Upper end of preferred rearing range of coho 58.3 14.3 Washington Dept. of Ecology standard (equivalent

MWAT calculated from annual max.) 57.7

14 57.2 13 Upper end of preferred rearing range for steelhead. 55.4

* 16.5 C MWMT corresponds with a 10% reduction in growth of coho. Modified from North Coast Regional Water Quality Control Board NMFS, National Marine Fisheries Service