Microhabitat Utilization and Fish Survey of the San ...Microhabitat Utilization and Fish Survey of...

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Microhabitat Utilization and Fish Survey of the San Antonio River

Glenn Longley John Burch Keith Cox

Chad Thomas

March 16, 1998

Edwards Aquifer Research and Data Center Southwest Texas State University, San Marcos, Texas

This project was supported by Texas Water Development Board

Interagency Contract No. 96-483-181

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TABLE OF CONTENTS 11\ iv'lAR 3 ':J 1998

II REGIONAL PLANNING 1-1

& i'ROJEorrs

TABLE OF CONTENTS ....•.•......•....•......•.•..•.•....•..•...•....•.............•......•....•.•..•.•....•.•.... 2

FIGURES ...................................................................................................................... 4

TABLES ........................................................................................................................ 5

APPENDICES ............................................................................................................... 6

1.0 EXECUTIVE SUMMARY ........•.•.•.•....•....•.•.•..•...•..•.•.•.••.•..•.•.•..•.•.•..•.•..•...•.•..•.•..•. 7

2.0 INTRODUCTION ................................................................................................... 7

2.1 Study Area .................................................................................................................................... 7

2.3 Protected Species .......................................................................................................................... 8

2.4 Climate .......................................................................................................................................... 8

2.5 Geology .......................................................................................................................................... 8

3.0 SITE SELECTION .................................................................................................. 8

3.1 Basic Strategy ............................................................................................................................... 8

3.2 Soil Associations ............................................................................................................................ 8

3.3 Hydrologic and Geomorphic Criteria .......................................................................................... 9

3.4 FIELD RECONNAISSANCE ................................................................................. 9

4.0 DATA COLLECTION ............................................................................................ 9

4.1 Bathymetric .................................................................................................................................. 9

4.2 Hydrologic ..................................................................................................................................... 9

4.3 Habitat assessment ........................................................................................................................ 9 4.31 Habitat Mapping and Photodocumentation ............................................................................. 10 4.32 Microhydraulic Effect of Habitat ............................................................................................ 10 4.33 Instream Habitat Classification ............................................................................................... 10

2

4.4 Biological Assessment ................................................................................................................. 21 4.41 Biological Indices ................................................................................................................... 21 4.42 Biological Sampling Techniques ............................................................................................ 21

4.5 Physicochemical .......................................................................................................................... 21

4.6 Biological Assessment of Habitat Utilization and Availability Conditions ................................ 21

5.0 RECOMMENDATIONS AND CONCLUSIONS ••.•.•.•.•••••.•.•.•.•.•.••.••.•.•.•.•••.•.•.•.• 27

6.0 REFEREN CES ...................................................................................................... 28

7.0 APPENDICES ....................................................................................................... 30

3

FIGURES

1. DAILY MEAN FLOWS AT USGS GAGE 08188500 AT GOLIAD, DURING STUDY PERIOD .....•.....•.......•.....•...........••....••.....•....••....••.....•.....•............•.....•..... 11

2. GENERAL STUDY AREA. SOURCE: USGs. .................................................... 12

3. GENERAL STUDY AREA (SITES 1, 2, 4, AND 5). SOURCE: USGS . .............. 13

4. SPECIFIC STUDY AREA (SITE 1). SOURCE USGS ......................................... 14

5. SPECIFIC STUDY AREA (SITES 2 AND 4). SOURCE: USGS . ........................ 15

6. SPECIFIC STUDY AREA (SITE 5). SOURCE: USGs. ...................................... 16

7. SKETCH MAP OF SITE 1. .................................................................................. 17

8. SKETCH MAP OF SITE 2 ................................................................................... 18

9. SKETCH MAP OF SITE 4 •.•.••..•.••••...••••...••..•.•.•••...•••••.•••••...•••....•••••...••..•..••••.•.•. 19

10. SKETCH MAP OF SITE 5 •..•.••..•••••.•.•••••...........••••...•••.....••••..•••••...•••....•••.•.•.•••... 20

4

TABLES

1. INDEX OF BIOTIC INTEGRITY (mI) FOR FISH COLLECTED 1996 AND 1997 ........................................................................................................................ 22

2. LIST OF FRESHWATER FISHES COLLECTED FROM THE SAN ANTONIO .RIVER SySTEM ................................................................................................... 23

3. PHYSICOCHEMICAL DATA FOR 1996 AND 1997, SAN ANTONIO .RIVER.24

4. FLOW DATA FOR MICROHABITATS ON SAN ANTONIO.RIVER FOR SITES 1,2,4 AND 5 DURING SUMMER 1997 ••••••..••.•....•...•••••••.•.•.•••......•........ 25

5. FLOW DATA FOR MICROHABITATS ON SAN ANTONIO.RIVER FOR SITES 1,2, 4 AND 5 DURING WINTER 1997 ..................................................... 26

5

APPENDICES

FISH SPECIES CODE FOR BUBBLE GRAPHS ..................................................... 31

MICROHABITAT CODE FOR BUBBLE GRAPHS ............................................... 32

BUBBLE GRAPHS ..................................................................................................... 33

REPRESENTATIVE PHOTOGRAPHS OF SAMPLE SITES ................................ 49

REPRESENT A TIVE MICROHABITAT PHOTOGRAPHS ................................... 53

6

1.0 EXECUTIVE SUMMARY

Studies in the West Central area of the Trans-Texas Program have considered possible alternatives for making more water available to the region and relieving demand on the Edwards Aquifer. One alternative is a proposed reservoir to be located on the San Antonio River near Goliad, Texas for water storage and diversion. The purpose of this study was to survey fish microhabitat utilization at study sites on the San Antonio River that will be utilized in the Texas Water Development Board's (TWDB) Macrohabitat Assessment Technique (MAT) for instream flow requirements. This study also used the Index of Biotic Integrity (IBI) proposed by Karr et al. (1986) to assess the water quality at the study sites and continued the listing offish species from this drainage. The species offish present in different habitats were determined. Physicochemical data was collected at each site during each sampling period.

2.0 INTRODUCTION

2.1 Study Area

The San Antonio River headwaters are located in the city of San Antonio, north of Brackenridge Park (Gonzales 1988). They originate from pumped wells drilled into the Edwards Aquifer. The topography at the sample sites consists oflow rolling hills. The riparian zone of the sample sites consisted of hardwood trees, vines, shrubs, and various weeds and grasses. Banks along the San Antonio River were generally high with steep sides.

The four sample sites are located in Goliad county. Much of the land surrounding the sites was used for agriculture (ranching) purposes.

Site 1 was located immediately upstream from the Hwy. 183 bridge in Goliad State Park, south of the city of Goliad. The USGS gage (08188500) used to monitor flows was located at this bridge. Site 2 was located 8 river km downstream of Site 1. Site 4 was located 4 river km downstream from Site 1. Access to Sites 2 and 4 was through the Baker Ranch located offHwy. 59, southwest of the city of Goliad. Site 5 was located immediately upstream from the Duke bridge on Hwy. 2506, south of the town of Fannin.

This study used fish species as biological indicators of water quality. The biological methods indicate that the stream at all sites had poor to fair water quality. Extensive laboratory chemical analyses were done on previous studies (Whiteside, et al. 1993 and Whiteside, et al. 1994). Temperature, dissolved oxygen, pH, and specific conductivity were recorded at each sample date.

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2.3 Protected Species

No endangered or protected species were found at these three sites. No effort was made to collect species other than fish.

2.4 Climate

All four San Antonio River sites are located in South Central Texas. The rainfall has varied greatly during 1996 and 1997 to the extent that this region experienced a drought and flood period within a 12 month period. The study area is humid subtropical with hot summers. Rainfall averages 33 inches annually and is heaviest in May and September (Mathews and Tallent 1996). The prevailing winds are southeasterly, often pushing warm, moist air from the Gulf of Mexico during spring, summer and fall. This leads to very sporadic rainfall, often from thunderstorms during these months. In the winter some Polar air flows into the area and is often stopped by warmer air off the Gulf. This usually results in mild winters. Rainfall during the winter is usually distributed along frontal boundaries, giving a more uniform coverage of rain than the thunderstorms that predominate during the rest of the year (Mathews and Tallent 1996).

2.5 Geology The river substrate consists of soft mud, sand, and silt along the edges and sand and small gravel in the middle of the channel. Pools and runs are the common morphological habitat types of the river. Rimes are rare except for small ones found along sharp, rocky bends. The water color ranges from a murky brown to a translucent green. Fallen trees, exposed roots, other woody debris, pools, and runs made up most of the microhabitats. Aquatic macrophytes are typically nonexistent, however, algae grows on some of the submerged rocks and trees (Findeisen 1997).

3.0 SITE SELECTION

3.1 Basic Strategy

An important step in environmental assessment of the aquatic communities is the selection of the study sites. TWDB staff required sites that had representative habitat and hydrologic conditions which would allow them to obtain information useful to their MAT protocol. TWDB staff participated in the selection of sites. Once sites were chosen, sampling began. Photos were made of the sites and of the microhabitats.

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3.2 Soil Associations The study area is located in the Coastal Plains area of the state. Soils near the river are dark gray to reddish brown calcareous clay loams and clays were prevalent (Arbingast, et al. 1976).

3.3 Hydrologic and Geomorphic Criteria

The intent of the study was to combine the reports of the San Antonio River fish sampling during winter and summer seasons at three different flow ranges: low (150-225 cfs), medium (225-300 cfs), and high (300-400 cfs).

3.4 Field Reconnaissance

As indicated under 3.1, both Edwards Aquifer Research and Data Center (EARDC) and TWDB staff were utilized to help locate suitable sites. Participating in this phase were Dr. Glenn Longley, Director ofEARDC at Southwest Texas State University (SWTSU), and two SWTSU graduate students, John Burch and Keith Cox. Ray Mathews, fisheries biologist/ecologist (Contract Manager), James Tallent, civil engineer; and Randy Bums, hydrogeologist participated from TWDB. The ecologists offered ideas of suitable microhabitats while the geomorphologists assisted in the determination of stream segments with several flow characteristics.

4.0 DATA COLLECTION

4.1 Bathymetric

This work is to be done by the TWDB.

4.2 Hydrologic

Additional work is to be done primarily by the TWDB staff. Information from the USGS gage 08188500 at Goliad, was used to determine when stream flow was within appropriate range for sampling to be performed. The daily mean flows for San Antonio River during 1996-1998 can be seen in Figure 1.

4.3 Habitat assessment

US Environmental Protection Agency (EPA), Texas Natural Resource Conservation Commission (TNRCC) and Texas Parks and Wildlife (TPWD) have been using illI protocols in the state to develop criteria for stream classifications (Bayer, et al. 1992). TWDB staff have developed their own system, known as MAT, for describing instream flow needs (Mathews and Bao 1991). This study utilizes the combination of illI protocols and MAT.

9

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z: ... 10000

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USGS 08188500 SAN ANTONIO RIVER AT GOLIAD, TX.

02/01/97 05/01/97 08/01/97 DATES: 09/01/1996 to 01/31/1998

Data is provisional and subject to revision. Source: USGS

11/01/97

Daily mean flows at USGS gage 08188500 at Goliad, during study period.

Figure 1.

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4.31 Habitat Mapping and Photodocumentation

Figures 2 and 3 show generalized maps of the study location. Figures 4,5,6 show the study sites on USGS quadrant maps. Figures 7,8,9, and 10 are sketch maps showing microhabitat locations within the study site. Numbers on the maps correspond with the microhabitat code found in Appendix 1. Representative photographs of the sample sites and microhabitats within those sites are found in Appendix 3.

4.32 Microhydraulic Effect of Habitat

This work is to be completed by TWDB staff.

4.33 lnstream Habitat Qassijication

Habitat is basically a locality, site or particular type of environment on a micro scale that is occupied by an organism or population of organisms.

11

General study area. Source: USGs. Figure 2.

12

·Nt SCALE: 1 INCH = 14,388 FEET

General study area (Sites 1,2,4, and 5). Source: USGs. Figure 3.

13

\ " I

Specific study area (Site 1). Source USGS. Figure 4.

14

Specific study area (Sites 2 and 4). Source: USGS. Figure 5.

15

di", II II II

" II II

'73

" ,Nt II \\

" II

" \I SCALE: I INCH"" 2,000 FEET

" " " II \I II -, " I " ,

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Specific study area (Site 5). Source: USGS. Figure 6.

16

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GOLIAD STATE PARK

46 8 13 4

Numbers correspond with microhabitat code numbers. (Site is 2,566 feet in length)

Sketch map of Site I.

Figure 7.

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HWY.183

13

8 4

4 13 4

13

Nt 1

FENCE


Sketch map of Site 2.

Figure 8.

18

BAKER RANCH

FLOW ).

Nt

15 13

8 6 14 4

4



Figure 9.

19

9 13 7

4

8

N'

13 23 16

134

8

13

DUKE BRIDGE



Figure 10.

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4.4 Biological Assessment

Water development projects such as the ones proposed alter the natural flow of the stream. It is important to know what the impact of the altered flows will be on the biological community. This information is important since it may be necessary to mitigate the effect of the altered flows by various management options.

4.41 Biological Indices

The indices used in this study have been developed by the EPA and modified for the purpose of categorizing stream segments. The water quality assessment technique chosen was the IBI found in Table 1. Reference streams were Arenosa Creek, Metate Creek, Placedo Creek, San Miguel Creek and West Caranchua Creek as used in previous studies of these sites (Whiteside, et aL 1993 and Whiteside, et aL 1994). A list of the fishes used in the IBI calculations can be found in Table 2. Additionally, the MAT methodology developed by TWDB was considered and the data was collected in such a way as to be useful for this type of technique.

4.42 Biological Sampling Techniques

The information gathered from sampling can be seen in bubble graphs which indicate the fish collected from different habitats (Appendices 1, 2, and 3). The Appendices include bubble graphs that represent individual sample dates and combined sampling dates from a previous study.

4.5 Physicochemical

The following parameters were analyzed in the field: temperature, pH, dissolved oxygen, specific conductance and flows at each microhabitat The results, for sampling done during this study are in Table 3. Flows for the individual microhabitats at each site are found in Tables 4 and 5.

4.6 Biological Assessment of Habitat Utilization and Availability Conditions

The TWDB staffwill complete this portion of the study utilizing MAT methods.

21

Table l. Index of Biotic Integrity (illI) for fish collected 1996 and 1997.

Site 1 Site 2 Site 4 Site 5 Sample Date: 3-Jan-97 I-Nov-97 I-Nov-97 I-Nov-97

Winter at med flows

Raw Metric Raw Metric Raw Metric Raw Metric Metrics Used: Score Score Score Score Score Score Score Score

Total # of Species 7 3 4 1 2 1 5 3 # of Darter/Catfish 2 3 0 1 0 1 3 Species # of Sunfish Species 1 1 1 0 # of Minnow Species 2 3 3 3 2 3 # of Intolerant Species 0 1 0 1 0 1 0 1 % Green Sunfish 0% 5 0% 5 0% 5 0% 5 % Omnivores 12% 5 30% 3 75% 7% 5 % Insectivores 46% 5 60% 5 25% 3 93% 5 % Top Carnivores 23% 5 10% 5 0% 0% Total # ofIndividuals 26 10 4 1 28 1 % Hybrids 0% 5 0% 5 0% 5 0% 5 % Diseased! Anomalies 0% 5 0% 5 0% 5 0% 5

IBI Score 42 36 28 38 Score Interpretation Fair Fair Poor Fair

illI = Index of Biotic Integrity

Site 1 Site 2 Site 4 Site 5 Sample Date: 9-Sep-97 9-Sep-97 10-Sep-97 22-Oct-97

Summer at bigh flows

Raw Metric Raw Metric Raw Metric Raw Metric Metrics Used: Score Score Score Score Score Score Score Score

Total # of Species 6 3 8 3 8 3 9 3 # of Darter/Catfish 2 3 2 3 2 3 2 3 Species # of Sunfish Species 1 1 3 3 3 3 4 3 # of Minnow Species 1 3 1 3 1 3 1 3 # of Intolerant Species 0 1 0 1 0 1 0 1 % Green Sunfish 3% 5 13% 3 13% 3 6% 3 % Omnivores 10% 5 13% 5 13% 5 11% 5 % Insectivores 31% 3 33% 3 33% 3 69% 5 % Top Carnivores 59"10 5 53% 5 53% 5 19"10 5 Total # of Individuals 29 1 15 1 15 1 36 1 % Hybrids 0% 5 0% 5 0% 5 0% 5 % Diseased! Anomalies 0% 5 0% 5 0% 5 0% 5

IBI Score 40 40 40 42 Score Interpretation Fair Fair Fair Fair

illI = Index of Biotic Integrity

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Table 2. List of freshwater fishes collected from the San Antonio River system.

Family

Lepisosteidae

Anguillidae

Clupeidae

Cyprinidae

Catostomidae

Characidae

Ictaluridae

Poeciliidae

Centrarchidae

Percidae

Cichlidae

Species

Lepisosteus oculatus

Anguilla rostrata

Dorosoma cepedianum

Campostoma anomalum Cyprinella lutrensis C. venusta Macrhybopsis aestivalis Notropis stramineus N. volucellus Pimephales vigilax

Jctiobus bubalus Afoxostoma congestum

Astyanax mexican us

Ameiurus melas A. natalis Jctalurus punctatus Pylodictis olivaris

Gambusia ajJinis Poecilia latipinna

Lepomis auritus L. cyanellus L. gulosus L. macrochirus L. megtalotis L. microlophus L. punctatus Aficropterus salmoides

Etheostoma cholorosomum E. spectabile

Cichlasoma cvanoguttatum

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Common Name

Spotted gar

American eel

Gizzard shad

Central stoneroller Red shiner Blacktail shiner Speckled chub Sand shiner Mimic shiner Bullhead minnow

Smallmouth buffalo Gray redhorse

Mexican tetra

Black bullhead Yellow bullhead Channel catfish Flathead catfish

Western mosquitofish Sailfin molly

Redbreast sunfish Green sunfish Warmouth Bluegill sunfish Longear sunfish Redear sunfish Spotted sunfish Largemouth bass

Bluntnose darter Orangethroat darter

Rio Grande cichlid

Table3. Physicochemical data for 1996 and 1997, San Antonio River.

Site Number Date pH S. Cond DO (mg/l) Temperature (C) (Ilmhoslcm)

1 1-3-97 8.4 726 8.2 19.9 9-10-97 8.1 957 7.0 28.7

2 9-9-97 7.4 1023 6.5 28.4 11-1-97 8.0 792 8.1 23.0

4 9-10-97 8.4 825 7.0 29.2 11-1-97 8.6 842 8.1 22.7

5 10-22-97 7.8 660 7.8 21.5 11-1-97 7.9 825 7.5 22.3

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... - -_._---_._--------

Table 4. Flow data for microhabitats on San Antonio River for sites 1,2,4 and 5 during summer 1997.

Microhabitat Site I 9-10-97 Site 2 9-9-97 Site 4 9-10-97 Site 5 10-22-97 Code ~th Flow DeEth Flow DeEth Flow ~th Flow

I 3.7 0.8 NA NA 3.0 0.2 NA NA 2 4.0 0.7 NA NA 3.0 0.5 NA NA 3 3.5 0.4 NA NA 4.0 0.1 NA NA 4 2.5 0.4 NA NA 2.5 0.3 NA NA 5 3.0 0.7 NA NA 2.0 0.2 NA NA 6 2.5 0.2 NA NA 1.5 0.1 NA NA 7 2.5 0.5 NA NA 1.0 0.4 NA NA 8 3.0 0.6 NA NA 2.0 0.2 NA NA 9 2.5 0.2 NA NA 3.0 0.2 NA NA 10 1.7 0.6 NA NA 3.5 0.3 NA NA 11 2.7 0.6 NA NA 3.0 0.0 NA NA 12 2.5 0.6 NA NA D D NA NA 13 2.5 0.9 NA NA 3.5 0.5 NA NA 14 3.0 0.8 NA NA NA NA 15 3.5 1.0 NA NA NA NA 16 1.5 0.3 NA NA NA NA 17 3.5 0.5 NA NA NA NA 18 3.0 0.0 NA NA NA NA 19 3.5 0.6 NA NA NA NA 20 3.0 0.3 NA NA NA NA 21 1.5 0.7 NA NA NA NA 22 1.0 0.3 NA NA NA NA 23 4.0 0.2 NA NA NA NA 24 2.5 0.6 NA NA NA NA 25 NA NA NA NA

Depth is in feet and flow is feet/sec. The character W reflects a washed out microhabitat. The character D reflects to deep to measure.

25

Table 5. Flow data for microhabitats on San Antonio River for sites 1,2,4 and 5 during winter 1997.

Microhabitat Site I 1-3-97 Site 2 11-1-97 Site 4 11-1-97 Site 5 11-1-97 Code Depth Flow DeEth Flow Depth Flow Depth Flow

I NA NA 4 0.8 4.0 2.0 3.0 0.1 2 NA NA 3 0.5 4.0 0.0 3.2 0.3 3 NA NA 3.5 0.1 4.0 0.0 4.0 0.2 4 NA NA 1.5 0.0 3.0 0.9 W W 5 NA NA 2.8 0.0 2.0 0.6 4.5 0.2 6 NA NA 3.5 0.2 3.0 1.7 5.0 0.3 7 NA NA 3.0 0.5 2.0 1.8 1.7 0.2 8 NA NA 2.6 0.3 2.7 1.3 3.5 0.8 9 NA NA 3.2 0.6 2.0 0.8 4.5 1.3 JO NA NA 1.5 0.1 3.5 1.3 1.5 0.3 II NA NA 1.0 0.4 2.0 0.0 4.5 I.J 12 NA NA 4.0 0.8 w w 2.0 0.7 13 NA NA 2.6 0.6 3.5 1.0 3.0 2.2 14 NA NA 3.2 0.6 2.5 1.8 4.5 0.3 15 NA NA 3.0 0.7 1.7 0.9 16 NA NA 2.0 0.6 5.0 0.8 17 NA NA 6.0 0.0 18 NA NA 2.2 I.J 19 NA NA 3.0 2.0 20 NA NA 2.0 0.5 21 NA NA 22 NA NA 23 NA NA 24 NA NA 25 NA NA

Depth is in feet and flow is feet/sec. The character W reflects a washed out microhabitat. The character D reflects to deep to measure.

26

5.0 RECOMMENDATIONS AND CONCLUSIONS

The data that was collected in this study will be incorporated with hydrologic and bathymetric data obtained by TWDB personnel and used in their MAT model. The MAT study reach model involves analysis of biological data from microhabitats at different flows, especially the distribution offish within those microhabitats at different flows, during summer and winter.

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6.0 REFERENCES

Arbingast, S. A., L. G. Kennamer, R. H. Ryan, 1. R. Buchanan, W. L. Hezlep, L. T. Ellis, T. G. Jordan, C. T. Granger and C. P. Zlatkovich. 1976. Atlas of Texas. Bur. of Bus. Research, Dniv. of Texas. Austin. Texas. 179 p.

Bauer, J., R. Frye and B. Spain. 1991. A natural resource survey for proposed reservoir sites and selected stream segments in Texas. Contract Rpt. #1756. TWDB. TPWD, Austin, TX. pp. 56-57.

Bayer, C. W., 1. R. Davis, S. R. Twidwell, R. Kleinsasser, G. Linam, K. Mayes and E. Hornig. 1992. An assessment ofleast disturbed streams (Draft). TWC, TPWD and USEPA Reg. VI. 406 p.

HDR Engineering, Inc. 1994. Trans-Texas Water Program - West Central Study Area Phase I Interim Rept. Vol. 2. SARA, SAWS, EUWD, GBRA, LCRA, BMWD, NRA and TWDB. 548 pp.

Jennings, M., D. Ockerman and D. Brown. Multidimensional hydraulic measurement and modeling for habitat assessment, Guadalupe River, Texas. United States Geological Survey. Unpublished.

Karr, J., K. D. Fausch, P. L. Angermeier, P. R. Yant, and I. 1. Schlosser. 1986. Assessing biological integrity in running waters a method and its rationale. Illinois Natural History Survey Publication 5, Champaign, Illinois.

Killebrew, F. C. 1991. Habitat characteristics and feeding ecology of Cagle' s map turtle (Graptemys cag/ei) within the proposed Cuero and Lindenau reservoir sites. Contract Rpt. #91-483-797. TWDB & TPWD. 15 p.

Linam, G. and R. Klinesasser. 1993. Draft trophic/tolerance designation of Texas fishes. Texas Parks and Wildlife Department, Austin, TX. 4 p.

Longley, G. 1997. IFIM - Phase I study, Guadalupe River. Edwards Aquifer Research and Data Center for Guadalupe-Blanco River Authority.

Longley, G., 1. Burch, K. Cox, and C. Thomas. 1998A. Microhabitat utilization and fish survey of the Guadalupe River. TWOB Contract No. 96-483-181.

Longley, G., K. Cox, 1. Burch, and C. Thomas. 1998A. Microhabitat utilization and fish survey of Cibolo Creek. TWOB Contract No. 96-483-181.

28

Longley, G., K. Cox, G. Phillips and 1. Miller. 1996. Environmental study of proposed diversion sites g-10 and g-14 on the Guadalupe River. TWDB Contract No. 95-483-113.

Mathews, R. c., Jr. and Y. Bao. 1991. Alternative instream flow assessment methodologies for warmwater river systems. Proc. Warmwater Fisheries Symp.1. Scottsdale, Ariz. pp. 189-196.

Mathews, R. c., Jr. and 1. R. Tallent. 1996. Instream flow assessment for the proposed Sandies Creek Reservoir. Texas Water Development Board. 72pp +53 pp. Appendices.

Platkin, J. L., M. T Barbour, K. D. Porter, S. K. Gross and R. M. Hughes. 1989. Rapid bioassessment protocols for use in streams and rivers: Benthic macroinvertebrates and fish. EP Al444/4-89-00 1.

Stalnaker, C. B., L. Lamb, 1. Henriksen, K. Bovee and 1. Bartholow. 1995. The instream flow incremental methodology - A primer for IFIM. BioI. Rpt. 29. Nat. BioI. Service, USDI, Washington, DC 45 p.

Whiteside, B. G., T L. Arsuffi. 1993. An aquatic inventory of the proposed Cibolo and Goliad Reservoir sites. TWDB Contract No. (92-93) 1071.

Whiteside, B. G., 1. A. Findeisen and V. Castillo. 1995. Microhabitat utilization and fish survey of Cibolo Creek and the San Antonio River. TWDB Contract No. 94-483-812.

29

7.0 APPENDICES

APPENDICES

30

Appendix 1. Fish species code for bubble graphs.

Code Scientific Name

2

3

4

5

6

7

8

9

10

II

12

13

14

15

16

17

18

19

20

21

22

23

24

25

26

27

28

29

30

31

32

33

34

35

36

37

38

Anguilla rostrata

Lepisosteus sp.

Dorasoma cepedianum

Aslyanax mexicanus

Hybopsis aestivalis

Cyprinella venusta

Cyprinella lutrensis

Notropis straminells

Notropis valucellus

Pimephales vigilax

Campostoma anomalum

Ictiobus bubaluslCyprinus carpio

Moxostoma congestum

Minytrema melanops

Ictalurus sp.

Pylodictis olivaris

Ameirus natalis

Fundulus notatus

Gambusia affinis

Poecilia latipinna

Menidia beryllina

Micrapterus punctlllatlls

Erimyzin oblongus

Micropterus treculi

Micrapterus salmoides

Lepomis gulosus

Lepomis cyanellus

Lepomis allritlls

Lepomis punctatus

Lepomis micralophus

Lepomis macrochirus

Lepomis megalotis

Pomoxis annularis

Pamoxis nigramaculatus

Percina macralepida

Etheostoma spectabile

Cichlasoma cyonoguttatum

Mugil cephalus

Common Name

American eel

Spotted/Longnose gar

Gizzard shad

Mexican tetra

Speckled chub

Blacktail shiner

Red shiner

Sand shiner

Mimic shiner

Bullhead minnow

Central stoneroller

Smallmouth buffalo/Common carp

Gray redhorse

Spotted sucker

Channe1lBlue catfish

Flathead catfish

YeHow bullhead

Blackstripe topminnow

Western mosquitofish

Sailfin molly

Inland sil verside

Spotted bass

Creek chubsucker

Guadalupe bass

Largemouth bass

Warmouth

Green sunfish

Redbreast sunfish

Spotted sunfish

Redear sunfish

Bluegill

Longear sunfish

White crappie

Black crappie

Bigsca1e logperch

Orangcthroat darter

Rio Grande cichlid

Striped mullet

31

Appendix I. Microhabitat code for bubble graphs.

Individual Graphs Code Microhabitat 1 Pool 2 Chute 3 Rapid 4 Pool - Root Wad 5 Edgewater 6 Run 7 Pool - Undercut Bank 8 Riffle - Bank Snag 9 Backwater 10 Riffle 11 Riffle - Debris dam 12 Riffle - Snag complex 13 Riffle - Channel snag 14 Eddy pool 15 Glide 16 Run - -Root Wad 17 Pool - Bank Snag 18 Pool - Undercut Bank 19 Pool - Snag Complex 20 Pool - Channel Snag 21 Pool - Debris Dam 22 Run - Debris Dam 23 Run - Bank Snag

24 Run - Channel Snag 25 Backwater - Channel Snag

32

o 12 3 4 567 8 91011121314151617181920212223242526

Microhabitat Code

Appendix 2. Site 1 at winter medium flow, Jan. 3, 1997.

33

38 37 36 35 34 33 32 31 30 29 28 27 26 25 24

Q) 23 "022 o 21 U 20 Ul 19 .~ 18 ~ 17 0.16

C/) 15 14 13 12 11 10

9 8 7 6 5 4 3 2 1 o

~ ~

u u u u

u U

--u- v

u ::: u u

U v v v

U

u :: u v

U v U v

U

v ~ .n v

-::aCa v

: .. .:.. ~

~ ::: v v v v v

u U U U

v v U

:: ~ :: :: v u u u

u U U

u v u u

• • v U v

::: IAv v v :.:.v v

v -v u v

u u v

n n n n ....... :: ~aCa .. .:.. u ~ • .:.

:: :: :: v v v v v

.n .a:a n . ,.,. v v u

'( ~ V U

I I I I

U·U U ~

:: :: u ~ ::

U -u

u U U U ·U

U U U ~ ~

v

u ~ u v ·U

U U U U ~ ;..

u v ~ ~ ~

U U U U ·U

v v V \F

·U ~ ;.. v u

~ ~

U U U v ·v

v U U \F

~ ~ ~ ~ ;; u :: ::

u ·U

v U v u- -v

:: ~ ~ u ::

.;;.;.~ U

-= r--aCa~~-1\ '--.. .:..: .. _y I~

u :: :: I • ., '--

v v v V ·v

u U U v -u-

~ ~

v ;;. v v v U ·u

v v u u

• n::: n

i-~ I--

u ~..-.a u

U~._ .. u I--

v V v i-v :: v v i-

V ~ V U u

:.a:a ~ -V

w; .. .... '( V U U ~ I I T T I

o 1 2 3 4 5 6 7 8 91011121314151617181920212223242526

Microhabitat Code

Appendix 2. Site 1 at summer high flow, Sept. 10, 1997.

34

38 37 36 35 34 33 32 31 30 29 28 27 26 25 24

Q) 23 "022 o 21 U 20 (/) 19 .~ 18 ~ 17 0.16

C/') 15 14 13 12 11 10

9 8 7 6 5 4 3 2 1 o

v v -v .,. v

-v v ;; ;:. n v v v v v

V V V V v

-v v Ie:· ~

-= n

v v

V v

v

v V ;; :' n v v V v v

V U vv v

v ::: ;:. ;:. n v v v v

V V V U" v

::: ::: .,- v

v v ::: ::: n V V U v v

v -v v

v v ;:. ::: n V V V V v

-v -v v ~ n v v ;:. ;:. u v v v v

V U -v U" V

n n ;;;; V

V V V v

-v v -u v v

., --v -v v

v v n

v v ;:: --v v

n v v

" u v V

V

n V V

V v ::. -v '{ I I I I I I I

o 1 2 3 4 5 6 7 8 91011121314151617181920212223242526

Microhabitat Code

Appendix 2. Site 2 at winter medium flow, Nov. 1, 1997.

35

38.-~'-r-(~-.-,~~.-.-~J-.-.~-r~'-'-'-~~~~ 37;-~+-~~~-+~~~+-~~-4-+~~4-+-+-~~-+~ 36;-~+-~(~~-+-~~4-+-~~-4-+~~4-+-+-~~-+~ 351-~+-~~-+-+~~4-+-~~-4-+~~4-+-+-~-4-+~ 34;-~+-~~-+-+~~4-+-~~-+-+~~4-+-+-~-4-+~ 334-~+-~~_+-+-~~4-+-

321-~+-~~-+-+~~4-+-311-~+-~~-+-+~~4-+ 304-~+-~~_+-+~~4-+-

291-~+-~~-+-+~~4-+-281-~+-~~-+-+~ 274-~+-~~_+-+~

264-~+-~~-+-+-o 251-~+-~~-+-+~~4-+-~~-4-+~~4-+-+-~-4-+~ 244-~+-~~-+-+~~4-+-~~-4-+~~4-+-+-~-4-+~

~234-~+-~~_+-+~~4-+-~~-+-+~~4-+-+-~-+-+~

u221-~+-~~-+-+~~4-+-~~-+-+~~4-+-+-~-+-+~ °214-~+-~~-+-+~~4-+-~~-4-+~~4-+-+-~-4-+~ U204-~+-~~_+-+~~4-+-~~-+-+~~4-+-+-~-+-+~ ~191-~+-~~-+-+~~4-+-~~-+-+~~4-+-+-~-+-+~ .~ 1 8 4--{)-+----,f-O-+_+_ ~ 17 4-~+-~~_+ 0..16 4-~+-~~--l-i en 15 4-~+-~~-+

14 -+--{)-+--If-O-+_+_ 13 -+~~~+-~ 121-~+-114-~+-1 04-~+-~~_+--, 94--{)-i---1f-O-+-84-~+-~~-74-~+-~~-64-~+-~~-

5 -I--O--+-f-O-+-4 4-~+-~~_+-' 34-~+-~~_+-+~~4-+-~~-+-+~~4-+-+-~-+-+~

21-~+-~~-+-+~~4-+-~~-+-+~~4-+-+-~-+-+~ 1--1-~+-~~-+-+~~4-+-~~-+-+~~4-+-+-~-4-+~ O--l-4-+-~~-+-+~~4-+-~~-+-+~~4-+-~~-4-+~

o 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 192021 2223242526

Microhabitat Code


36

38 37 36 35 34 33 32 31 30 29 28 27 26 25 24

Q) 23 "022 021 (,) 20 II) 19 .~ 18 ~ 17 0.16 en 15

14 13 12 11 10

9 8 7 6 5 4 3 2 1 o

" " " ~ ~ ~

v u u ~ " v v v v v V V V

u v u V v -v -v v

"V ~~ " ::: ::: ::: " " " ::: "

v ::: v v v v v v u u v

v v v v u V -v-

~ ~ ~ ~ ~ ~ ~ :::

;:: ;:: " ;:: " v ;:: v

v v v u u u u v

"V" "V u v v -v -v v

::: " u " v ::: v

v v v u v V V V

V V V V v -v v-v

u v ;:: v " u :: v

u v u u u u v v

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;:: " " " " ~ ~ "

u v v v v v v v

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" ~~;;v -v -v

v ;:: " ;:: " .;. " ::

v v v v v V V v

"V" -v v v u v v v

v ::: " ::: " .;. " ::

v v v v v u v u

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v

u u v v v v v v

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:: " ;: ::I .;. ::: :::

::r v v v

-v v -v

rI<, '-: '-: I I I I I I I I

o 1 2 3 4 5 6 7 8 91011121314151617181920212223242526

Microhabitat Code


37

38.-,-.-~r.~-fr-~~'-.-~~~~-'-.~'-.-r-~~-' 37;-~+-~~-fr~-~~+-+-t-()~~-+~~+-+-~~-4-+~ 36;-~+-~~-fr~~~+-+-~}-C~-+~~4-+-~~-4-+~ 35;-~+-~~~-fr~~~+-+-1~(~-+-+-r~+-+-r-~-+~ 344-+-+-~~-fr-~~~+-+-~)-C~-+~~4-+-~~-+-+~ 33 +-+-f-t-D--+-O 32 -+-+-+---1--0--+-..0 31 -+-+-+---1--0--+-.0 30 +-+-+--1'-O-+-1C 29-+-+-+--28-+-+-+-, 27-+-+--H 26-+-+-+-, 25-+-+--H 24-t-+-+

Q) 23+-+-+~22-+-+-+--~~-fr~~~+-+-~~~--+--r~+-+-+--~~-+~ °21+-+-+-~~-fr~~~+-+-~}-O~-+-r~+-+-+-~-+-+~ °20+-+-+-~~-fr~~~+-+-~~~-+~~+-+-+-~-+-+~ til 19 -+-+-+-: .~ 18-+-+~17+-+-0.16-+-1-en 15-+-+-

14-+-+-13+-+-+-c 12-+-+--H 11-+-+-+-' 1 0 -t-+-t-, 9+-+-8-+-+-7-1-l-6-+-1-5-+-+-4-t-+-t-' 3+-+-+-c 2-+-+-+ 1-+-+-+-' O+-+-+-

o 1 234 567 891011121314151617181920212223242526

Microhabitat Code


38

38 37 36 35 34 33 32 31 30 29 28 27 26 25 24

CD 23 "'C 22 o 21 t) 20 III 19 .!!! 18 ~ 17 0.16

C/) 15 14 13 12 11 10

9 8 7 6 5 4 3 2 1 o

" " " " " " " v ""vv

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v v laa " v

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'7 '7 v '7 v Y v Y '7 '7 \ \ I I t I I I I \

o 1 2 3 4 567 8 91011121314151617181920212223242526

Microhabitat Code


39

38 37 36 35 34 33 32 31 30 29 28 27 26 25 24

Q) 23 u 22 o 21

C,.) 20 VI 19 .!!! 18 l6 17 0.16 (J) 15

14 13 12 11 10

9 8 7 6 5 4 3 2 1 o

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v v '( V

,- -, ,- T

o 1 234 5 6 7 8 91011121314151617181920212223242526

Microhabitat Code

Appendix 2. Site 5 at summer high flow, Oct. 22, 1997.

40

38.--~.-~~~~~-~-,~~~~~~-,~~~~~(~~~ 371-~+-r4~~~~~~~~~~-+~~~+-+-~~-+~ 361-~+-r4~~~~~~~~~~-+~~~+-+-~~-+~ 354-~+-~~~-o~~~~&-~~~-+-~~~+-~~-4~ 344-~+-~~~-o-~~~-o-D~~~~-+~~4-+-~~~~ 331-~+-r4~~-~~~~~~~~-+~~~+-+-~~-+~ 32~~+-~~-o~-~~~~~~~-+~-~4-+-+-~~-+~

311-~+-r4~-o~~~~~~~~-+~4r~+-+-~~-+~ 301-~+-~~~~~~~~~~~-+~~~+-+-~~-+~ 291-~+-~'114~~4r~~~1~~~-+~~~+-+-~~-+~ 28~~+-~~-o~~~~~~~~-+~~4-+-+-~~-+~

274--~+-~~~-o~1IHr~-o-~~~~-+4r~4-+-~~~~ 261-~+-~~~~4r~~~~~~-+~~~+-+-~~-+~ 25~~+-~~-o~~~~~~~~-+~~4-+-+-~~-+~ 24~~+-~~-o~~~~~~~~-+~~4-+-+-~~-+~

~231-~+-~~~~4r~~~~~~-+~~4-+-+-~~-+~ ~22~~+-~~~~4r~~~~~~-+~~~+-+-~~-+~ o 21 +--{)-t--1I-O

C,.) 20 -+--0-+--+--0-Ul 19 ~-(}-.f--II-(} .~ 18 -+-.Q--I--+~ ~ 17 +-~t--1I--O--': 0. 16 -+--o-~ en 1 5 -I---(}-f---lj

14 -+--o-t-+ 13+-~+--1 2 -+-111 ... -1---.

11 -+-:O:-l--f 101-~+--9~~+-8 -+-.Q--I--7-+--o-\-J 6 -+--O-j-.: 5 -I---(}-.f--I~~-o.O:--{] 4 ~~~~~~4--(}-+-~~-+-+~~+-~

3 2 1+-~+-~~~~~~~~~~~-+~~4-+-+-~~-+~ 0+-+-+-~~-+-+-r~+-+-~~-+-+~~4-+-+-~-+-+~

o 1 234 5 6 7 891011121314151617181920212223242526

Microhabitat Code

Appendix 2. Site 1 at medium f10VIIS, July 15,1994 and Jan. 3,1997.

41

38 37 36 35 34 33 32 31 30 29 28 27 26 25 24

Q) 23 "022 o 21

C,,) 20 U) 19 .!!! 18 ~17 0.16

C/') 15 14 13 12 11 10

9 8 7 6 5 4 3 2 1 o

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n v

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v

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n

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n

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n

n n n n n ;. n n n n n ::: v ::: v ::: ::: OJ

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OJ

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n

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I I I 1 , I T

o 1 2 3 4 5 6 7 8 91011121314151617181920212223242526

Microhabitat Code

Appendix 2. Site 1 at high flows, Dec. 15, 1993 and Sept. 10, 1997.

42

38.-~.-,-(r.~-.-~~'-~~~~-.-r~~~~~~~~ 37~~+-~~~-+~~1--o-~1~~-+-+~4-+-+-~~-+~ 36~~+-~~~-+~~1-~~~~-+-+~4-+-+-~~-+~ 35~~+-~~~-+~~4-~~~~-+-+~4-+-+-~~-+~ 34~~+-r-(~~-+~~~~~~~-+-+~1-+-+-~~-+~ 33~~+-~~~-+~~~~~~~-+-+~4-+-+-~~-+~ 32 ~~+--h<J..-t~-31 -+--~+-""'1a-1~-30~~+-~~~-29~~+-~~~-+~~4-~~~~-+-+~4-+-+-~~-+~ 28-+--~+-~~~-+~4r~~~~~-+-+~-+--+-+-~~-+~

27-+--~+-~~~-+~4r~~~~~-+-+~-+--+-+-~~-+~

26~~+-~~~-+~~~~~~~-+-+~-+--+-+-~~-+~ 254-~+-~~~-+~~4-~~~~-+-+~4-+-+-~~-+~ 24-+--~+-r-1~~-+~~~~~~~-+-+~-+--+-+-~~-+~

m23~-o-+-~~~-+~~~~~~~-+-+~-+--+-+-~~-+~ u224-~+-~~~-+~~4-~~~~-+-+~-+--+-+-~~-+~ °21-+--~+-~~~-+~4r~~~~~-+-+~-+--+-+-~~-+~ U20~~+-~~~-+~~~~~~~-+-+~-+--+-+-~~-+~ Ul 194-~+-~~~. ~ 1 8 -+---(}--+-I--{)f~ 17 -holrt--t Q. 16 ~.1.c.l...-en 1 5 -I-'"!JE-+-

14 -+--D-f-+--<l-' 13 -I--G-+--4-{}-' 12 -I--G-+---l-{}-11 -I--{)-+--4-{}-1 10-+--~+-~~~-+~~-I-~~~

9~~+-r-(~~-8-+--~+-7-+--~+-

6~~+-5 4--O-+-~~~"""; 4 -+---(}--+--1 3~~+-2-+---o-+-1 4-~+-~~...3I(j~ 04-~+-~~~-+-r-r4-+-+-~~-+-+~4-+-+-~~-+-1

o 1 2 3 4 5 6 7 8 91011121314151617181920212223242526

Microhabitat Code

Appendix 2_ Site 2 medium flows, July 14,1994 and Nov. 1, 1997_

43

38 37 36 35 34 33 32 31 30 29 28 27 26 25 24

Q) 23 "022 o 21 U 20 U) 19 .~ 18 ~ 17 0.16

(f) 15 14 13 12 11 10

9 8 7 6 5 4 3 2 1 o

n n " n " "

n

n .~. n n ::: ::: ;. n

n ~~, v v v

n n n n

n n n n n ;.. ::: ::: n n n n ::: ::: n

V V v

n n n n .v. ::: ::: v v v

n n n

;. .:. n .:. n n

n t:...

n ';,." n n ":..' ::: ::: n n n ::: n ::: ::: vv

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n n n n n n n n n n V V V V v ::: v v v

n n n n n n ;::' ~ ~ n

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V

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\ \ 1 I I I \ \ \ I

o 1 2 3 4 5 6 7 8 91011121314151617181920212223242526

Microhabitat Code

Appendix 2. Site 2 at high flows, Jan. 7, 1994 and Sept. 9, 1997.

44

O uuu~ ~ uu

I I I I 111 I I 1 I

o 1 2 3 4 5 6 7 8 91011121314151617181920212223242526

Microhabitat Code

Appendix 2. Site 4 medium floVIIS, July 14, 1994 and Nov. 1, 1997.

45

38 37 36 35 34 33 32 31 30 29 28 27 26 25 24

Q) 23 "022 o 21

C,.) 20 I/) 19 .!!! 18 ~ 17 0.16 en 15

14 13 12 11 10

9 8 7 6 5 4 3 2 1 o

~ ~ " " " v

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v v v v v v ~ ~ "

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V

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v v v J IV v",,:,, v

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" n n n n n

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h h V

~ . : .. n .. : .. V ~':. " ,,~:... n n " ~ v v :: .q v :: :: n • • ~ .. " " • • 111 I J I .II: ..

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h h

V V V

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~ " n " 'w;:.,

V V V , V ~ I , 1 1 1 1 -I r 1

o 1 2 3 4 5 6 7 8 91011121314151617181920212223242526

Microhabitat Code

Appendix 2. Site 4 at high flows, Jan. 10, 1994 and Sept. 10, 1997.

46

Q) "0 o U Ul Q) '(3 Q) a. en

38 37 36 35 34 3

31 30 29 28 27 26 25 24 23 22 21 20 19 18 17 16 15 14 13 12 11 10

9 8 7 6 5 4 3 2 1 0

~ ~ ~ ,.. ... ... n 1'\ ~ ~

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n

n

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v -v -V-Vvvv v v v

n n n

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n ~ ;. ~ " ;. n ~ ~ n n ~ v

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-v v v v v v v

n n ~ ~ ~ ~ ." " " " " ::: ~ ;, I A " n n n " n

v -v ~ n

v ~ n

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:: '""",,~ " " " --"- t}~"n;: ;: n n

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n n ~ -/1. --f\ --''L'';''' ~ ~ ~ ~. ~.. n n n n n n v v

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n v v

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~ ~ ; ~ I I ,- ,- ,- T I I I I I I

o 1 2 3 4 5 6 7 8 91011121314151617181920212223242526

Microhabitat Code

Appendix 2. Site 5 at medium flows, July 13, 1994 and Nov. 1, 1997.

47

38 37 36 35 34 33 32 31 30 29 28 27 26 25 24

CD 23 "022 a 21 U 20 Ul 19 .~ 18 ~ 17 0.16 en 15

14 13 12 11 10

9 8 7 6 5 4 3 2 1 o

n

n

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n

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Microhabitat Code

Appendix 2. Site 5 at high flows, Jan. 10, 1994 and Oct. 22, 1997.

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Site 1 - Upstream View

Site 1 - Downstream View

Appendix 3. Representative photographs ofsamp\e sites.

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Appendix 3. Representative photographs of sample sites.

50




51




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Root Wad

Run

Appendix 4. Representative microhabitat photographs.

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Undercut Bank

Bank Snag


54

Backwater

Snag Complex


55

Channel Snag

Eddy Pool


56

Pool-Root Wad

Pool-Bank Snag


57

Pool-Undercut Bank

Pool-Channel Snag


58

Run-Bank Snag

-


59

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