Broad Timescale Forcing and Geomorphic Mediation of Tidal ...tidal dynamics at hourly, lunar,...

Broad Timescale Forcing and Geomorphic Mediationof Tidal Marsh Flow and Temperature Dynamics

Christopher Enright & Steven D. Culberson &

Jon R. Burau

Received: 29 June 2012 /Revised: 17 April 2013 /Accepted: 21 April 2013 /Published online: 8 May 2013# The Author(s) 2013. This article is published with open access at Springerlink.com

Abstract Tidal marsh functions are driven by interactionsbetween tides, landscape morphology, and emergent vegeta-tion. Less often considered are the diurnal pattern of tideextremes and seasonal variation of solar insolation in themix of tidal marsh driver interactions. This work demonstrateshow high-frequency hydroperiod and water temperature var-iability emerges from disparate timescale interactions betweentidal marsh morphology, tidal harmonics, and meteorology inthe San Francisco Estuary. We compare the tidal and residualflow and temperature response of neighboring tidal sloughs,one possessing natural tidal marsh morphology, and one that ismodified for water control. We show that the natural tidalmarsh is tuned to lunar phase and produces tidal and fortnightwater temperature variability through interacting tide, meteo-rology, and geomorphic linkages. In contrast, temperaturevariability is dampened in the modified slough whereoverbankmarsh plain connection is severed by levees. Despitegeomorphic differences, a key finding is that both sloughs areheat sinks in summer by latent heat flux-driven residual up-stream water advection and sensible and long-wave heattransfer. The precession of a 335-year tidal harmonic assuresthat these dynamics will shift in the future. Water temperatureregulation appears to be a key function of natural tidal sloughsthat depends critically on geomorphic mediation. We investi-gate approaches to untangling the relative influence of sun

versus tide on residual water and temperature transport as afunction of system morphology. The findings of this studylikely have ecological consequences and suggest physicalprocess metrics for tidal marsh restoration performance.

Keywords Tidal marsh .Water temperature . Tidalharmonics . Geomorphology . Hydroperiod

Introduction

Tidal marshes are the most vulnerable estuarine systemhabitats. They occupy the transition between open waterand terrestrial systems. They are defined by the presenceof tidal creeks, marsh plains, and emergent vegetation thatabsorb energy, exchange nutrients and sediment, and generallyproduce system carbon (Mitsch and Gosselink 2007; Kneib etal. 2008). Process feedbacks between tide, sediment, and veg-etation dynamics make each component at once system driver,and system function (Reed 1988; Friedrichs and Aubrey 1988;Silvestri and Marani 2004; Kirwan and Murray 2007). Theseinteractions generate sharp residence time and scalar gradientsand ecotonal diversity (McLusky and M. Elliott 2004). Theirvulnerability arises from the inconvenience they place on hu-man access to navigable channels valuable for transportation,food, and waste disposal (Vileisis 1999). As a result, mosttemperate estuaries have lost much of their tidal marshes tohuman development (Holland et al. 2004). The San FranciscoEstuary (SFE) has lost between 80 % (Monroe et al. 1999) and95 % (Atwater et al. 1979) of its historical wetland extent.

Tidal marsh-to-channel interactions are the loci of keyestuarine ecosystem functions including regional food websupport through export of excess productivity to net consum-er habitats (Cloern 2007; Kneib et al. 2008), and provision offorage, cover, and reproduction space habitat for resident andmigratory fishes (Knieb 1997; Simenstad et al. 2000).

C. Enright (*)California Delta Stewardship Council/Delta Science Program,980 9th Street, Sacramento, CA, USAe-mail: [email protected]

S. D. CulbersonUS Fish and Wildlife Service, 650 Capitol Mall, Sacramento, CA,USA

J. R. BurauUS Geological Survey, 1280 Terminal Street, West Sacramento,CA, USA

Estuaries and Coasts (2013) 36:1319–1339DOI 10.1007/s12237-013-9639-7

Spatiotemporal variability in tidal marsh function is usuallyattributed to tide, meteorology, and estuary inflow variability(Moyle et al. 2010). Underappreciated to this point is the roleof hydroperiod—the temporal pattern of overbank flooding—intidal marsh function (Malamud-Roam 2000). Overbank marshplain flooding processes are driven by interactions betweendifferent timescales of tidal dynamics and tidal marsh morphol-ogy that, in turn, influence high-frequency variability of tidalmarsh function. This paper investigates the influence of anadditional century-scale tidal oscillation that, when superimposedon annual, fortnight, and tidal timescale oscillations, produceshigh-frequency water temperature variability in tidal marshes.We review estuarine tide dynamics and tidal marshhydrogeomorphology and temperature dynamics as a foundationfor results and discussion.

Tides In this paper, we investigate the influence of geomor-phology and tidal hydroperiod on flows and temperature fluxesin nearby tidal sloughs. Like most coasts of the Earth, the SFEexhibits mixed semi-diurnal tides with two unequal high tidesand two unequal low tides per 24.84 h lunar day (Walters andGartner 1985). The harmonic pattern is a mixture of periodicforcings caused by the position, rotation, and altitude of theEarth relative to the sun and moon (Cartwright 1999). Theobserved tide is a superposition of harmonic frequencies gener-ated by aspects of the gravitational interaction between sun,moon, and earth. The speed of propagating tidal waves arecontrolled by water depth according to {g(h+z)} 1/2 where g isgravity acceleration, h is average depth, and z is wave height.Estuarine tides are distorted from their regular ocean harmonicsby shallow and variable morphology, river flow, and wind thattransfer some of the tidal energy into higher frequency“overtides” (Parker 2011). This distortion is especially impor-tant in natural tidal marshes where morphology strongly medi-ates hydroperiod (Malamud-Roam 2000; Aubrey and Speer1985). There is also a consistent seasonal pattern of diurnal tideextremes caused by slight differences in tidal harmonics thatadvance the daily tide 12.42 h while retreating the tropicalfortnight cycle 11.45 h (Malamud-Roam 2000). As a conse-quence, the net change in the annual sequence of the diurnaltidal pattern is about 1.09 days/year with a full cycle period of335 years. This pattern has consequences for estuarine processesthat are mediated by sunlight. Examples include biochemicalprocess rates in mudflats as affected by diurnal timing of tidalexposure and estuarine monitoring that could be biased by thetiming of sampling regimes. Finally, as we will demonstrate,this low frequency tide oscillation influences estuarine watertemperature dynamics.

Tidal Flow Asymmetry Discounting watershed inputs, thetotal discharge through a tidal slough cross-section is equalto u(t)×A which, integrated over a tidal cycle, is nominallyequal to zero (where u is cross-section average velocity and

A is cross-section area). However, estuarine tides aredistorted by processes that compete to produce either fasterflood or ebb currents (Friedrichs and Aubrey 1988). Whenthe duration of ebb tide is shorter than flood tide, strongerpeak ebb currents compensate and the system is consideredebb dominant. The opposite is true for shorter duration floodtides (Walton 2002). Residual sediment transport is sensitiveto the tidal velocity pattern, thus system bathymetry isstrongly influenced by ebb-flood asymmetries (Friedrichsand Perry 2001; Dronkers 1986). Tidal asymmetries canalso arise from other interacting processes including variabilityof estuarine morphology (Fischer et al. 1979; Dronkers 1986),phasing of principle tidal constituents with their higher har-monics (Aubrey and Speer 1985; DiLorenzo 1988), and chan-nel friction and depth relationships (Aubrey and Speer 1985).The San Francisco Estuary is possibly unique because itsoverall ebb dominance arises from tidal harmonic content thatsequences the low–low tide after the high–high tide about 80%of the time (Malamud-Roam 2000). Consequently, tidal currentmaxima occur most often on ebb tides with clear implicationsfor sediment and chemical–biological transports. At the tidalslough scale, flow and velocity asymmetry can also be drivenby natural tidal marsh morphology where channel marginsgenerally orient to approximately local mean higher–highwater(MHHW).

Tidal Marsh Hydrogeomorphology Tidal marsh geomor-phology characteristically includes a nearly level vegetatedplain incised by a terminal dendritic channel network(Myrick and Leopold 1963). The marsh plain elevation istypically near the upper end of the tidal frame and constitutes ahydrogeomorphic threshold for several marsh processes andfunctions (Pethick 1980). High tides that exceed bank-fullelevation rapidly expand the flow area and generate muchstronger currents in marsh channels resulting in flood domi-nant current asymmetry (Reed 1988; French and Stoddart1992). Lawrence et al. (2004) reports measurements ofunder-marsh plain tidal flows that generally peak near1/3 m/s while over-marsh tidal currents with sudden accessto the marsh plain can exceed 1 m/s for short periods. Inremnant natural marshes of Suisun Marsh California(Fig. 1), about 15 % of high tides flood over channel banks.A smaller percentage of high tides flood marsh plains consid-erably, primarily by stronger full moon spring tides in thesummer and winter.

Tidal Marsh Temperature Budget Tidal marsh water andsoil temperature is regulated by heat flux at the air–landand air–water interface and is mediated by tidal dynamicsand marsh morphology (Wheaton 1977; Hardisty 2999;Stacy and Monismith 2008). The temperature budgetincludes several interacting processes: solar insolation asshort wave radiation is directly absorbed by water and

1320 Estuaries and Coasts (2013) 36:1319–1339

modulated by turbidity, cloud cover, and reflectivity. Netlong-wave radiation is a measure of the difference betweenoutgoing long-wave heat radiation from land and water andincident atmospheric long-wave counter-radiation. Directconduction of heat across the air–water interface (sensibleheat flux) depends on the interface temperature difference.Wind speed and fetch are key mediators of this process.Water evaporation drives latent heat flux to the atmospheredepending sensitively on relative humidity, water tempera-ture, and wind. Finally, water temperature transport is con-trolled by river flow (advection) and tidal currents(dispersion). McKay and DiIorio (2008) identified distinctsections of a tidal creek with a different mix of temperaturedrivers depending on tidal creek morphology and tidal com-munication with the adjacent bay. Along-creek temperaturegradients are tidally mixed by bathymetry and curvature-induced lateral and vertical water column shear (Rattray andDworski 1980). Temperature gradients are also mixed byebb and flood flow asymmetries between dendritic creeks anddistributary channels, a process called tidal trapping (Fischeret al. 1979). Depending on diel timing, sediments exposed atlow tide can develop steep vertical subsurface temperaturegradients that dissipate rapidly under subsequent inundation(Harrison and Phizacklea 1987). On vegetated marsh plains,the temperature budget depends sensitively on the particularplant species present as they can alter evaporation and mediatesolar insolation and wind at the air–water and land–waterinterface (Crabtree and Kjerfve 1977).

Native species have adapted life history and phenotypicstrategies to physical process patterns in natural estuaries.Restoration of physical process and pattern is a key toconservation of native estuarine species in modified

estuaries (Wiens 2002). Restoration performance measure-ment depends on understanding how landscape patternsmediate transport processes and outcomes like tidal marshslough currents and temperature regimes. The present anal-ysis compares how the disparate morphologies of nearbysloughs control hydroperiod and thus water exposure tosolar insolation and heat exchange processes. Natural tidalmarshes display a sharp elevation discontinuity at the inter-section of channel edge and marsh plain. This drives a step-change in hydroperiod on the highest tides which periodi-cally increase water exposure to air temperature and sun.Sun exposure in natural marshes is modulated by phasing oftidal dynamics at hourly, lunar, seasonal, and decadal time-scales. We demonstrate how these processes become damp-ened and irregular in diked sloughs. By comparing twosloughs with essentially matching driver influence and sim-ilar relative size, we assume that all differences in internalflow and temperature dynamics are ultimately due to mor-phology differences. We investigate several approaches tountangling the relative influence of meteorology versus tideon residual water and temperature transport as a function ofsystem morphology.

Study Area

Suisun Marsh is the largest contiguous brackish water wet-land in California. It is in the geographic center of the SanFrancisco Estuary downstream from the Sacramento–SanJoaquin River Delta and upstream from the San FranciscoBay (Fig. 1). It comprises about 30,000 acres of sloughs andsmall bays, about 52,000 acres of managed wetlands, and

Fig. 1 Study area and sensor locations in Suisun Marsh, California. To indicate the contrast between sloughs compared in this paper, a nominalcross-section elevation for each slough is shown relative to NGVD88 and key tide height constituents

Estuaries and Coasts (2013) 36:1319–1339 1321

about 6,300 acres of mostly unmanaged tidal marsh. It is animportant wetland on the Pacific Flyway, providing foodand habitat for migratory birds. The managed wetlands aremostly duck hunting clubs that have seasonally controlledwater through levee culverts for 80 to 120 years. As else-where around the world, wetland water control has causedwidespread land subsidence from compaction and peat soildecomposition (Turner 2004; Portnoy and Giblin 1997). Bycontrast, the remnant tidal marshes largely maintain historicalgeomorphic characteristics including dendritic tidal creek sys-tems, steep sided channels, low creek-side levees withrelatively higher mineral composition, and marsh plainsthat maintain elevation near mean higher–high water(Culberson et al. 2004).

These contrasting land uses provide an opportunity tocompare hydrogeomorphic functioning as a consequenceof land use. Sheldrake Slough (SH) and First MallardBranch (FM) in Suisun Marsh offer just such a comparison(Fig. 1). SH is a former tidal creek system modified withinthe last century for duck hunting club water management. Atleast three slough orders and the associated marsh plain havebeen severed from the main slough. The remaining mainslough is completely diked from the mouth to a cul-de-sac-like terminus at its western end, a distance of about 1.7 km(Fig. 1). Hydraulic connectivity to the surrounding land isthrough several culverts with screw gates and flashboardrisers to control water levels. Surrounding lands are moder-ately subsided from their late Holocene elevation near localMHHW (approximately 2.1 m NAVD88 today). By com-parison, FM has not been diked and thus maintains naturalfeatures including low natural levees on tidal creek banksand a marsh plain elevation near MHHW. It is a fourth-ordertidal creek system connected to a small managed ephemeralcreek watershed that contributed essentially zero inflowduring the study period. The main slough is approximately2.7 km from mouth to upland creek transition. The MLLWdepth is 1 to 1.5 m over most of the length. The average SHtidal prism is about 86K m3, about 69 % of the sloughvolume of approximately 123K m3 below mean high water.The average FM tidal prism is 40K m3, about 77 % of theslough volume of approximately 58K m3 below mean highwater.

Methods

High-frequency flow and constituent concentration measure-ments are widely used in tidal areas to estimate material fluxes(e.g., Reed 1988; French and Stoddart 1992; Temmerman et al.2005; Lucas et al. 2006). We obtained time series of specificconductance, water temperature (T), and current velocity (U) at15-min intervals the mouths of FM and SH between April 15and August 5, 2004 (n=10,752). We used Argonaut XR 3-

beam current meters at both sites sensing at 1,500 kHz. Thecurrent meters were attached to frames for stability. A 30-mcable attached the current meter frame to a 100- kg weight. Asurface mark also attached to the weight (Fig. 2). The samplingperiod for the current meter was 600 s and the averaging periodwas 240 s. The instruments were powered by a 100 amp/hbattery enclosed within the frame. A time series of slough flowwas generated from stage-area measurement and index velocityrating.

Multi-parameter sondes were co-located with the currentmeters so that constituent fluxes could be calculated (Fig. 2).We used battery powered YSI 6600 sondes deployed nearlow tide mid-depth (approximately 1 m off the bottom).Sondes were attached to steel cables and suspended fromunderwater buoys. Fifty-kilogram weights anchored theapparatus. A 30-m stainless steel cable connected the sondeapparatus to a 100 kg weight that anchored a marker buoy(Fig. 2). The sonde was programmed to log dissolved oxygen(optical), temperature, specific conductance, and unventeddepth, every 15 min. The sondes were serviced and datadownloaded approximately once every 10 days. Equipmentfailures occurred occasionally due to probe leakage, and bio-fouling. We also obtained 15-min tide stage for the mouth ofthe estuary at the GoldenGate (USGSweb access), and hourlyreference evapotranspiration (ETo) and air temperature frommeteorology station within 3 km of the sloughs (DWR 2011).All references to “15-minute” data in this paper refer to theraw, unfiltered data.

A primary aim of our data analysis is to unravel the suite ofshifting and interacting driver influences on slough temperatureand currents. These understandings are essential for judging theperformance of tidal marsh restoration initiatives in estuaries.Our approach is to investigate candidate meteorology and tidedriver proxies with principle components analysis, then calcu-late non-parametric slough current and temperature responsecorrelations over a range of leads and lags. We further examinedrivers and responses by spring and neap tide categories todiscern how tidal dynamics and geomorphic thresholds influ-ence current and temperature response. Highest correlationleads or lags are submitted again to PCA to resolve relativedriver influences. We show that tidal flows and temperatures inthe sloughs are strongly driven by tidal harmonic forcing anddaily solar insolation. However, for subtidal timescales (greaterthan ∼1 day), slough flows and temperatures are driven bycomplex and shifting interactions between heat transfer mech-anisms and tide-morphology interactions.

We refer to flow and temperature responses at thesubtidal timescales (diel—24 h, and tidal—24.84 h) as “re-siduals” (after Walters et al. 1982); 24.84 h is two-times theM2 (principle lunar) tidal harmonic frequency which ac-counts for about 30 % of the total tidal amplitude potentialin Suisun Bay where the tidal content is considered “mixedsemi-diurnal” (Malamud-Roam 2000). We closely examine


residual flow and temperature responses to forcing by dielaverage meteorology and tidal day average RMS tide height atthe Golden Gate. The proxy for meteorological forcing is the24-h average of hourly reference ETo. We examine the effectof the drivers individually using non-parametric correlation,and in tandem using principle component analysis. When theresidual driver is 24 h average ETo, the flow and temperatureresponses are the 24 h average of 15-min data. When theresidual driver is 24.84 h average RMS tide height at theGolden Gate, we take several steps. First, we calculateGGRMSht=<(ht−hm)2>1/2 where GGRMSh is the RMS tideheight at the Golden Gate, ht is the 15-min Golden Gate stage(NAVD88) time series, hm is the least squares fit of GoldenGate stage for the study period, and < > denotes a low-passtidal filter (Godin 1972). Second, we tidally (low-pass) filterthe temperature and flow response data for each slough.Finally, we take the 24.84-h averages of GGRMSh and thetidally filtered flow and temperature responses by interpolat-ing between the 15-min data and sampling at 24.84-h inter-vals. Some of the analyses below investigate how residualflow and temperature responses differ between spring andneap tides. Tide categories were determined by fitting a linearregression to the calculated GGRMSh. Where regression re-siduals are positive, FM and SH flow and temperature data iscategorized as “spring tide” data. Where regression residualsare negative we assign response data to the “neap tide” cate-gory. In addition, we generate advective and dispersive waterand temperature flux estimates using the low-pass tidal filter.Finally, in all results below, the positive flow direction isdown-slough, or ebb direction, toward the ocean.

Tidal Timescale Results

Fifteen-minute flow time series for both sloughs are shownin Fig. 3a, b. Panel (c) shows the primary low frequency

physical drivers–RMS tide height at the mouth of the SanFrancisco Estuary (GGRMSh) and daily reference EToalong with moon phase. The common x-axis covers theperiod of the study between April 15th and August 5,2004. Both FM and SH tidal flow (shown in dark gray)varies between about −10 and +10 cm during lunar minima.There is a two- to threefold expansion of the tidal flow atFM during lunar maxima when water elevation exceeds themarsh plain elevation and conveyance area expands (Fig. 3panel a). FM flow is distinctly flood dominant reaching∼30 cm on flood tides compared to ∼20 cm on ebb tides.Flood dominance increases as astronomical tide strengthand variability increases into the summer. In contrast, SHresponds only minimally to spring tides with a slight flowrange expansion similar to the general estuarine spring tidalprism expansion. Spring tide maximum flow range at SH isabout ±12 cm.

Figure 4 magnifies a 14-day period between June 22 andJuly 6. Panel (a) shows the unvented depth (not tied to adatum) above the pressure sensors at the mouth of bothsloughs. The sensor depths at FM and SH are not identicalbut the graphical overlay masks differences. Panel (a) alsodepicts the approximate elevation of the natural levee at FMand the constructed levee at SH relative to the NGVD88datum. Since the y-axis is local sensor depth, it is notcommensurate with the NGVD88 levee elevations. Never-theless, the graphical comparison of heights illustrates thefrequency, magnitude, and duration of natural leveeovertopping. Finally, panel (a) shows the RMS tide heightat the Golden Gate. Panel (b) shows tidal flow detail for FMand SH. Three to four days prior to the maximum springtide, local tide elevation at FM is sufficient to overtop theslough bank (June 27, 10:15 PM) when there is a sharpincrease in flood tide flow. The site demonstrates an asym-metrical ebb-flood pattern as the ensuing ebb tide returns asharp yet lower magnitude and longer duration discharge.

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Strong flood dominance develops over the following 5–6 days.SH shows no such geomorphic flow mediation and the ebb-flood asymmetry is instead slightly ebb dominant. Panel (c)shows the concurrent water temperature response. On June 28,FM ebb discharge is cooled nearly 2 °C compared to 24 h prior.Between late afternoon on June 26 and early morning on June28, diel temperature differences approach 6 °C. The tidal pre-cession moves timing of overbank flood tides to 3:00 AM byJuly 4, the last day of overbank tide heights (Fig. 4). Ebbdischarge cooling is increasingly attenuated by morning sunexposure. SH exhibits a similar but damped pattern. FM alsoexhibits high-frequency (∼8-h period) variability within the dielwater temperature oscillation during the neap tide period (Fig. 4,∼June 22–26). Using a particle tracking model, we confirmedthat there is strong tidal trap due to the particular connectivity ofthe downstream distributary channel that alternately pulses wa-ter from different locations within the same flood or ebb se-quence. Tidal trapping dissipates during the ensuing spring tidewhen water volumes are more energetically mixed and tidalexcursions exceed distributary slough lengths (Fischer et al.1979; Warner et al. 2002). The underlying temperature signalat both sloughs is strongly forced by diel solar insolation duringboth spring and neap tides. Maximum and minimum tempera-tures generally occur at the end of ebb tide—minimum if theebb occurs predominantly at night, maximum if the ebb occurspredominantly during the day. Even on neap tides, flood-ebbtemperature oscillations are more than 4 °C.

Figure 5 accentuates the influence of slough morphologyby comparing tidal scale water depth and temperature

variability to tidal flow magnitude. Panels (a) (FM) and (b)(SH) show marked difference in the flow–depth patternespecially when tide level exceeds the local MHHW stageduring spring tides (approximately 2.1m NAVD88). Tidalflow increases rapidly with depth as the level exceeds thebank-full height. Flow variability is highly limited at SH bylevees. Panels (c) and (d) show the concurrent watertemperature pattern compared to flow. The core flow–temperature pattern is similar at each site until springtides drive flows over the bank and FM water temper-ature drops rapidly on the ensuing early morning ebbtides for several days.

Figure 6 shows tidal timescale flow distributions for eachslough categorized by spring and neap tides. The box plotsshow that SH exhibits little difference between spring and neapflow distribution characteristics while flow variability expandsmarkedly at FM on spring tides compared to neap tides.Reflecting the time series pattern in Fig. 3, flow extremes atFM occur on flood tides. The positive (ebb directed) medianflow shows that higher magnitude flood flows are balanced bylonger, lower magnitude ebb flows. Average FM spring tideflow is −0.43 cm (flood direction) while neap tide average flowis slightly positive (ebb direction). In contrast, average SH flowis always negative (flood direction). Figure 6 shows the com-panion tidal timescale water temperature data at the mouths ofthe sloughs. Mean and median temperatures between sloughsare well within one degree centigrade.

There is also a marked difference in the internal correla-tion structure of the tidal temperature signal between the

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Fig. 3 Tidal and residual flow(left axis), and cumulativevolume (right axis) betweenApril 15 and August 4 for FirstMallard Branch (a) andSheldrake Slough (b). Tidalflow is 15-min data. Residualflow is derived from a low-passfilter and multiplied by 10 toexaggerate the pattern.Cumulative volume is runningvolumetric sum of 15-min databeginning April 15. Negativevalues are flood direction (intoslough). Positive values are ebbdirection (out of the slough).Panel (c) is RMS tide height atthe Golden Gate and day totalETo 3 km northwest of site.Moon phase is shown forreference


sites. Figure 7 illustrates how temperature autocorrelationchanges through the spring-neap cycle by sliding the autocor-relation functions successively by 3 days (as Lucas et al.2006). Overall, FM remains smoothly auto correlated between24 h (diel cycle) and ∼24.84 h (lunar cycle) regardless of lunarstatus. Close inspection of the FM signal reveals a consistentpeak squarely between the solar and lunar forcing periods. Bycontrast, the SH peak autocorrelation is near 24.84 h duringspring tides and 24h during neap tides. SH periodicity alsomodulates strongly with lunar status becoming more irregularduring spring-neap transitions.

Subtidal Timescale Results

Meteorology and tide drivers also force ecologically impor-tant slough temperature and flow dynamics at subtidal,timescales. To compare processes between the natural and

modified slough, we computed water and temperaturefluxes, low-pass filtered residual flows and temperatures,and mean diel flows and temperatures. We also comparedthe distributions of tidal and diel average flow and temper-ature. Finally, we compared the shifting relative influence oftide and meteorological influence during spring and neaptidal conditions.

Figure 3 shows low-pass tide filtered flow for both sites(panels (a) and (b)—thick line). Tidally filtered flow at FMresponds consistently to lunar phase—always negative (flooddirection) during spring tide and positive (ebb direction) dur-ing neap tides. In contrast, SH shows little concordance withlunar phase. Indeed, the sign of tidally filtered flow is oftendifferent between the sites. The right axis of Fig. 3 panels (a)and (b) shows the cumulative water volume flux beginningfrom zero on April 15 (the negative trending traces). Over112 days, both sloughs accumulate somewhat more than twomillion cubic meters of water, though the accumulation

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Fig. 4 FM and SH slough mouth depth, flow, and temperature datafrom June 22 to July 6 2004. Panel (a) is 15-min local depth (notreferenced to a vertical datum) above unvented pressure sensorsmounted near the channel bottom. Note that slough depths are nearlyidentical and thus overlay. Right axis is RMS tide height at the GoldenGate. Panel (a) also shows the estimated NAVD88 elevation of theconstructed levee at SH, and the natural levee at FM relative to thelocal tide height. Panel (b) shows 15-min time series and tidal filtered

residual flow for both sloughs. Residual flows are multiplied by 10 forclarity. Panel (c) shows 15-min time series and tidal filtered residualtemperature for both sloughs. The first overbank flow of the spring tideoccurs on June 27 at 10:15 PM. The ensuing ebb tide flow (dottedvertical lines) is significantly cooled. The diel precession of overbankflows shifts the timing of ebb flows to the late morning reducing thecooling effect. Moon phase is depicted for reference


pattern is quite different. At SH, the net accumulation patternis nearly monotonic (approximately 18K m3/day) with

minimal rate response to lunar phase. Water diversions toadjacent managed wetlands may account for some of the trend

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Fig. 5 Flow vs. depth at themouth of First Mallard Branch(a) and Sheldrake Slough (b).Flow versus temperature at themouth of First Mallard Branch(c) and Sheldrake Slough (d).Dashed arrow on panel (c)indicates spring tidetemperature trajectory withflow. Data is 15-min data fromJuly 15 to August 4 2004.Depths are local (unventedpressure sensor). Bank-fullheight designation is estimated

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x = 20.5 = 2.06

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x =-0.43 = 7.26

x = -0.14 = 5.73

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x = -0.31 = 4.87 σ σ σ σ

σ σ σ σ

Fig. 6 Distribution of 15-minflow and water temperature datafor First Mallard Branch andSheldrake Slough. Data iscategorized by spring and neaptide. Box plot panels showmedian, and inner quartiles.Whiskers include the full datarange


though we would expect this forcing to produce a far morepulsed pattern than observed. Water management diversionsare usually minimal in late spring and zero in summer. Bycontrast, FM accumulates water at approximately 110–125Km3/day for 7–8 days on the stronger full moon spring tidesthen reverts to nearly zero water flux for about three weeksduring the two neap cycles and the weaker new moon springtide cycle when water levels do not exceed the natural tidalmarsh plain height. Panel (c) shows moon phase, GGRMSh,and the nearby ETo reference. The FM drainage is approxi-mately 300 acres. If we assume the total water flux over thestudy period is driven by latent heat transport and planttranspiration, then ETo would need to average about1.5 cm/day to account for the observed accumulation. Refer-ence ETo shown in Panel (c) ranges between 0.5 and0.8 cm/day. Using crop coefficients for typical wetland plantsincluding Scirpus species commonly found at FM we wouldexpect evapotranspiration between 1.2 and 1.8 cm/day (e.g.,Allen et al. 1992) which would place our estimates in areasonable range.

Comparing Water and Temperature Flux Concurrent mea-surements of high-frequency flow and temperature allowedus to estimate tidally averaged temperature flux (Fig. 8). Toclarify transport mechanisms, we decomposed the total tem-perature flux into advective and dispersive components (e.g.

Dyer 1973; Fischer et al. 1979). Total temperature flux isdecomposed as advective flux—the product of tidally fil-tered discharge and temperature (<Qt> <Ct>), and dispersiveflux—the tidally averaged product of high-frequency devi-ations from the tidal filter (<Qt′×Ct′>). Quantities inside < >are tidally averaged using a low-pass filter by the method ofGodin (1972). Total flux [C m3/s] is shown in black, tidallydriven dispersive flux is shown in green (the trace that staysnear zero), fluvial input or latent heat transfer driven advec-tive flux is shown in blue. Temperature flux at FM is clearlycoherent with lunar phase as maximum advection is up to anorder of magnitude larger than the period-average advec-tion. Concordant with water advection (Fig. 3), FM temper-ature advection is upstream (negative) on spring tides anddownstream (positive) on neap tides. Temperature disper-sion at FM is negative throughout the period (mean=−1.3C m3/s). Two types of dispersion peaks are evident. First,there is a strong correlation between advective and dispersiveflux during lunar maximums. This stronger dispersion peak islikely due to current shear associated with increased velocityduring overbank flow events. The dispersion is in the up-stream direction because the highest velocities occur on theflood tide. There is a secondary dispersive peak between newand first quarter moons that we hypothesize is correlated withthe tidal trap-induced along-slough temperature gradients(Fig. 4). In contrast, temperature dispersion at SH is small in

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Fig. 7 Progressive 3-day water temperature autocorrelation between June 21, and July 11. Each autocorrelation is based on 3 days of 15-mintemperature data. Vertical lines delineate diel (12–24 h) and tidal (12.42–24.84 h) periods. Moon phase is depicted for reference


magnitude (mean=−0.2 Cm3/s) and alternates sign irregularlythough the autocorrelation function is significant at the spring-neap cycle frequency. Temperature advection is primarilyflood directed and only minimally coherent with lunar status.Importantly, all temperature flux components for both sloughsare, on average, flood directed, suggesting that tidal sloughsare temperature sinks regardless of morphology and by morethan one mechanism.

Comparing Means and Distributions Comparing thesloughs at slightly different subtidal timescales reveals theinfluence of geomorphology. Solar insolation and subtidaltide drivers have closely phased harmonics at 24 h versus∼24.84 h but the dissimilarity in geomorphology betweenthe sloughs is sensitive to the difference. Table 1 compares

means and cumulative density functions for the observed15-min flow and water temperature data averaged, in turn,over tidal (24.84 h) and then diel (24 h) time scales. We alsodivided the data into spring and neap categories. At the dieltimescale, the means and CDF’s of 24-h average FM and SHtemperatures are not significantly different regardless of tidestatus. When the averaging period is only 3 % longer(24.84 h versus 24 h) all water temperature means andCDF’s become significantly different. Thus, meteorologicalforcing tends to equalize the temperature response betweensloughs at the diel scale while the interaction of tides andgeomorphology tends to differentiate the temperature re-sponse between sloughs at the tidal scale. As for flows,geomorphology differences make diel and tidal averageflows different in all cases except the neap tide diel CDF.

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April 2004 | May | June | July | August

Tem

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*m3 /

s)

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Fig. 8 Temperature flux at FM(a) and SH (b). Qt is 15-minflow; Ct is 15 min watertemperature; Qt′ is 15-min flowdeviation from tidal average; Ct′is 15-min deviation from thetidal average (Godin filter). < >is Godin filter. FM means(C m3/s): total flux=−5.8;advective flux=−4.6; dispersiveflux=−1.3. SH means: totalflux=−4.8; advective flux=−4.6;dispersive flux=−0.2. Moonphase is depicted for reference

Table 1 Comparing FM and SH flow and temperature means andcumulative density functions categorized by spring and neap tide.“Tidal day average” is 24.84 h average of 15-min data. “Diel average”is 24-h average of 15-min data. “Different” means that the mean or

CDF is different at the 0.95 level. Means are compared using Welchmodified two-sample t test; CDF’s are compared using Kolmogorov–Smirnov test

Tidal day (24.84 h) average Tidal day average flow Tidal day average temperature

Compare mean Compare CDF Compare mean Compare CDF

Spring tide Different Different Different Different

Neap tide Different Different Different Different

Diel (24 h) average Diel average flow Diel average water temperature

Compare mean Compare CDF Compare mean Compare CDF

Spring tide Different Different Same Same

Neap tide Different Same Same Same


Comparing the Relative Influence of Driver Native specieshave adapted life history and phenotypic strategies to physicalprocess patterns in natural estuaries. Restoration of physicalprocess and pattern is a key to conservation of native estuarinespecies in modified estuaries (Wiens 2002). Restorationperformance measurement depends on understanding howlandscape patterns facilitate processes and outcomes likecurrent and temperature structure. We investigated thesubtidal timescale influence and interaction of the tideand meteorology drivers using principle components tochoose among candidate tidal and diel average driverproxies. We considered but ruled out local tidally filteredwater depth for the tidal forcing proxy because depth at FMis distorted by local bathymetry and consistently “capped”when flow goes over bank. We instead use GGRMSh becauseit presents an unambiguous measure of subtidal astronomicalforcing compared to local depth. GGRMSh is also indicativeof tidal average estuarine elevation as it oscillates betweenspring and neap tides. We also examined air temperature andreference ETo as climate forcing variables. Principle compo-nents of air temperature and ETo were similar (not shown) butwe carried ETo forward in the analysis assuming it enfoldsmore comprehensive heat flux mechanisms including air tem-perature, humidity, and wind.

In each of the analyses that follow, the tidal residualresponses of flow and temperature are correlated at thesame timescale as the driver. When the residual driver is24-h average ETo, the flow and temperature responsesare the 24-h average of 15-min data (beginning May 1,n=98 days). When the residual driver is 24.84-h aver-age RMS tide height at the Golden Gate, flow andtemperature responses are the 24.84-h average of tidal(low-pass) filtered flow and temperature data (beginningMay 1, n=94 “tidal” days).

Table 2 shows correlations of residual flow and watertemperature to GGRMSh and ETo. By this simple measure,FM residual flow is driven primarily by tide strength whileSH residual flow is weakly but significantly driven by bothETo and GGRMSh. Temperature at both sloughs is notsurprisingly driven by ETo by this measure. Looking moreclosely, we did not expect that flow and temperature re-sponses would be instantaneous. For example, overbankflows were observed days in advance of the highest tides

when water elevation exceeded slough bank heights. There-fore, while we expect tide strength to drive slough flow andtemperature, geomorphic interactions induce response leadsand lags at the mouth of the sloughs where we deployedsensors. Figure 9 therefore expands the Table 2 analysis intwo dimensions. First, we examine responses to the drivervariables over a continuous span of leads and lags (on the x-axis). Second, we partition the data into spring and neap tidecategories based on the strength of Golden Gate RMS tideheight as explained in the methods section. Each triangle inFig. 9 represents an individual non-parametric correlationbetween driver and lagged response. Several patternsemerge.

1. Considering the driver-response relationships in Fig. 9as a whole, spring versus neap tides produce differentresidual temperature and flow responses in the sloughsthat can lead or lag the driver impulse. The individualdriver effects are broadly similar, though intermediatemechanisms may differ.

2. Neap tide residual slough flows are driven by both tidestrength and meteorology. The pattern of response overthe range of leads and lags is similar between the sloughssuggesting that the influence of morphology is minimizedwhen tide strength is low and high tides do not reach themarsh plain threshold (compare Fig. 9, N1–N2; N5–N6).Less energetic neap tides increase water residence timeand temperature (late spring/summer) and allow time forlatent heat-driven evaporation and evapotranspirationthat, in turn, induces upstream advective water flux.

3. Spring tide residual flows are dominated by tide strengthat both sloughs though the response mechanisms andpattern are quite different (compare Fig. 9 S1 and S2).FM residual flow is strongly inverse-correlated withspring tide strength. Maximum inverse correlation leadsGolden Gate RMS tide because high tides flood naturalmarsh plains 1–3 days before peak tides. This morpho-logical control is not present a SH which is mostuncorrelated exactly at peak tide strength because thedominant residual flow mechanism is the rate-of-changein lunar cycle estuary filling and draining—which be-comes zero at maximum (or minimum) RMS height. Thismechanism is equally at play at FM but morphology

Table 2 Correlation of drivers and responses. Response data is the diel average when correlated with 24-h average ETo, and the 24.84-h average oftidally filtered data when correlated with 24.84-h average Golden Gate RMS stage. The correlation coefficient is Kendall’s tau

Correlation with 24.84 h or 24 h flow Correlation with 24.84 h or 24 h temperature

FM SH FM SH

24.84-h average Golden Gate RMS Stage −0.81 (p<0.05) −0.27 (p<0.05) 0.03 (NS) 0.11 (NS)

24-h average ETo −0.06 (NS) −0.37 (p<0.05) 0.68 (p<0.05) 0.62 (p<0.05)


mediated tidal asymmetry dominates residual flowdynamics.

4. The pattern of residual temperature response to meteo-rological forcing (as ETo) is similar between the sloughs(compare Fig. 9, S7 and S8; N7 and N8). This is likelybecause meteorology is autocorrelated day-to-day sotemperature correlation to ETo can persist over severaldays—more so during neap tides when there is lessmixing with downstream distributary channels.

5. While there is no significant residual temperature re-sponse to GGRMSh at either slough (though some lagsare significant at the 0.10 level), the pattern across lagsis nevertheless instructive (compare Fig. 9, S3–S4; N3–N4). In general, the lag 0 correlation is near zero. Tidaldays in advance of minimum and maximum tidestrength tend to be positively correlated with GGRMShwhile tidal days after are negatively correlated in arather smooth pattern. Given the enormous heat capac-ity of the estuarine-scale water volume, some lag and“memory” in the temperature response to tide strengthmight be expected. The pattern suggests that residualwater temperature depends weakly but predictably on

the fortnight estuary fill-drain cycle with warming afterneap tides and cooling after spring tides. In the neap tidecase, weak tides can be considered a kind of “necessarycondition” supporting the persistent ETo–temperaturecorrelation (Fig. 10, N7–N8). The authors have noticedthat many water temperature monitors in the northernreach of the SFE show the same pattern of temperatureelevation on neap tides and reduction on spring tidessuggesting that evaporative cooling processes are stron-ger when surface water is mixed by more energeticcurrents on spring tides.

While Fig. 9 attempts to sort out the independent influ-ences of tide strength and meteorology on slough residualflow and water temperature, covariation interactions remain.In particular, Fig. 9 only hints at the residual flow andtemperature response to shifting combinations of driverstates. For example, we might expect the combination ofweak tides and high ETo to drive flows and temperaturesdifferently than weak tides and lower ETo. Similarly wewould expect the combination of strong tides and highversus low ETo would drive differential responses,

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Fig. 9 Correlation between drivers and lagged responses categorizedby spring and neap tidal periods. Lags are examined from negative(lead) to positive (lag). Each triangle is an individual non-parametriccorrelation between a driver (either Golden Gate RMS tide height[GGRMSh] or ETo) and response (residual flow or temperature). Whencorrelated with GGRMSh, all data is 24.84-h average of tidally filtereddata (n=94 tidal days). The corresponding lags are 24.84-h “tidal”

days. When correlated with ETo, all data is 24-h average of 15-mindata (n=98 days) and lags are 24-h days. Blue triangles are significant(p<0.05). Correlation statistic is Kendall’s Tau. Data is 5/1/04 to 8/4/04. FM is First Mallard Slough; SH is Sheldrake Slough. Dashed linesidentify zero lag and zero correlation. Orange circles identify lagssubmitted to PCA analysis in Fig. 10


especially at FM where morphology allows more driverinteraction. We attempted to partition the data into thesefour driver permutations but the analysis produced limitedinsight apparently because the drivers themselves co-varysomewhat. While the drivers are fundamentally indepen-dent, ETo is a proxy for meteorological processes that caninfluence tide heights through wind set-up and fetch orien-tation as well as atmospheric pressure and ocean tempera-ture anomaly. Finally, the correlation analysis tells us littleabout the shifting relative influence of the drivers duringspring and neap tides.

We submitted the drivers and maximum lead or lagresidual flow and temperature response from Fig. 9 (delin-eated by circles) to a principle components analysis forinsight into their variance explanatory power. An exceptionis the day-average water temperature–ETo correlation dur-ing neap tides (Fig. 9, N7 and N8). Water temperaturedisplays a multiple day “memory” of ETo due to the com-bination of longer neap tide residence time, the heat capacityof water, and the tendency for ETo to be autocorrelated overseveral days. We submitted to PCA the local peak correla-tion lags nearest to lag 0 to maintain a reasonable number ofobservations (realizations are lost as lags match up missingdata with observations that must then be dropped). To the

PCA, we chose to submit the lag 1 FM temperature–ETo,and lag 3 SH temperature–ETo correlations. We found thatresults are insensitive to perturbations around this choice.Figure 10 broadly verifies the pair-wise correlations inFig. 9 with some key clarifications.

Figure 10 demonstrates that both GGRMSh and EToinfluence residual temperature and flow outcomes. More-over, the interactions of driver effects, mediated by mor-phology, differentiate the slough responses. Depending onspring or neap tide status, one driver can dominate or bothcan share influence only to shift as the spring-neap tidalharmonic oscillates. Note that the drivers (ETo andGGRMSh) are not correlated so the PCA enforces a nearlyorthogonal ordination between them. This somewhat con-founds the graphical representation of flow and temperatureresponse components that are influenced by both drivers.We include the third component axis to help untangle thisambiguity. We consider spring and neap tide categories inturn.

Spring Tide Residual Flow On spring tides, FM residualflow is dominated by tide strength (Fig. 10, S1) with onlyweak influence by ETo primarily along the component 3axis (which explains only 5 % of the variance) (Fig. 10, S2).

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Fig. 10 Principal componentsof driver and lead/lag responserelationships. Response leads orlags are maximums fromcorrelation analysis in Fig. 9(orange circles). The first threecomponents are representedalong with variance explained.Left hand column is spring tides;right hand column is neap tides.When correlated with GGRMSh,all data is 24.84-h average oftidally filtered data (n=94 tidaldays from May 1). Thecorresponding lags are 24.84 h“tidal” days. When correlatedwith ETo, all data is 24-h averageof 15-min data (n=94 days fromMay 1) and lags are 24 h days.Response variables are identifiedby the averaging period (24.84 hor 24 h), the two-letter locationabbreviation (“FM” or “SH”)appended to a responsedescriptor, Q for flow, T fortemperature, and the lead or lagvalue. For example, themaximum correlation betweenGGRMSh and FM residual flowduring spring tides occurs 1 daybefore the maximum RMS tideheight, or “24.84hFMQlead1”


In contrast, ∼3-day lag SH residual flow is driven aboutequally by ETo and GGRMSh on spring tides (Fig. 10, S1)while components 2 and 3 emphasize the influence ofGGRMSh primarily along the component 2 axis (Fig. 10, S2).

Neap Tide Residual Flow On neap tides, SH residual flow(at both lag-0 day and lead-1 tidal day) is dominated by tidestrength with ordination primarily along the component 1axis (42 % of variance) (Fig. 10, N1). ETo influence onlead-1 tidal day SH flow appears on the components 2 and 3axes though the lag-0 day SH is not swayed by either driver(Fig. 10, N2). In contrast, lead-1 tidal day and lag-0 day FMresidual flow is influenced about equally by ETo andGGRMSh (Fig. 10, N1).

Spring Tide Residual Temperature Spring tide residualtemperature at both sloughs is dominated by meteoro-logical forcing as represented by ETo (Fig. 10, S1–N1).The component 2 and 3 axes demonstrate considerableadditional influence of GGRMSh on FM temperature,likely by the interaction of morphology and spring tideheights (Fig. 10, S2).

Neap Tide Residual Temperature On neap tides, residualtemperature at both sloughs is dominated about equally byETo (Fig. 10, N1). Reduced tidal range and less energetictidal flow dynamics equalize the driver influence on theotherwise disparate slough morphologies. A summary ofdriver influences and geomorphic interactions on residualflow and temperature outcomes is presented in Table 3.

Discussion

We contrast a natural and a modified tidal slough to comparethe effect of slough geomorphology and hydroperiod ontidal and residual water temperature and flow. At any giventime, slough water temperature and flow is influenced by theinteracting and shifting influence of sun (as meteorologyand tide) and moon (tide). Marsh morphology mediatesthese dynamics on timescales from hours to centuries viathe influence of hydroperiod. The effect of morphology isparticularly evident in the natural slough where lunar phaseand diel timing of tidal extremes strongly influences tidaland residual flow and temperature. Comparing sloughs, weshow that the natural slough is primarily driven by tidaldynamics and meteorology with substantial mediation bycharacteristic slough morphology. In contrast, the modifiedslough is influenced by tide and meteorology but there is farless interaction between drivers. This uncoupling of driverinteraction is due to the substantial disconnection of sloughwater from the marsh plain by levees thereby diminishing thehydromorphological linkage between tide and meteorology.

Thus, while the sloughs have essentially identical tide and suninfluence, the emergent flow and temperature dynamics aredifferent in possibly ecologically significant ways. We note inparticular the possible modification of water quality charac-teristics in water that remains on the tidal marsh plain betweenoverbank tides at FM. Water reaching the marsh plain onspring tides remains ponded or shallowly infiltrated throughsuccessive days and hosts biological activity throughout theperiod. One of the authors routinely observed amphipods andother aquatic invertebrates using ponded marsh plain habitatduring the intertidal period between spring tides in marshesthroughout the San Francisco Bay region (Culberson et al.2004). We speculate that primary productivity is enhancedwhere a slough network includes fortnightly overbank tidesas part of its underlying hydraulic character and see evidenceof chlorophyll a subsidy from this water as it drains back to thetidal slough network on the subsequent spring sequence(Enright et al., unpublished data). This aspect has not beenexplored conclusively in this report, but is the subject of futureanalysis.

At the subtidal timescale, residual flow is driven bysuperposition of three interacting processes. First, tidal flowasymmetries emerge from interaction between sloughmorphology and semi-diurnal tide dynamics. Second,residual flows track the fortnightly estuarine fill-and-drain cycle at the lunar timescale. Third, residual flowis forced by diel-to-seasonal evaporation and evapotranspirationwithin the slough drainage. In parallel, residual water tempera-ture is driven by heat flux from solar insolation, climate factors(wind and humidity), and hydroperiod mediated by morpholo-gy. Our analysis attempts to untangle the relative contribution ofthese influences to slough flow and temperature. We also inves-tigated possible lagged flow and temperature responses, bothpositive (lag) and negative (lead).We hypothesize that observeddifferences in flow and temperature response between naturaland modified sloughs is ultimately due to how morphologymediates tide, meteorology, and climate drivers.

Untangling Influences and Interactions We attempted tounderstand the suite of shifting and interacting driver in-fluences on slough temperature and currents. Our approachwas to choose among candidate meteorology and tide driverproxies with PCA, then calculate non-parametric responsecorrelations over a range of leads and lags on data dividedinto spring and neap tide categories (Fig. 9). Best leads orlags were submitted again to PCA to resolve relative driverinfluences (Fig. 10). Tides and diel meteorological forcingare closely phased in a ∼29-day precession of moon-suninteraction permutations. Concurrently, semi-diurnal tidalextremes generate shifting degrees of water exchange withthe downstream distributary channel. The influence of solarinsolation on water temperature depends partly on the resi-dence time of water in the slough which in turn depends on


Tab

le3

Sum

maryof

subtidal

timescale

driver

andresidu

alflow

andtemperature

respon

sesandinteractions.“R

esidual”

refers

tobo

ththe24

.84haverageof

tidal

filteredflow

ortemperature

respon

setoRMStid

einfluence,andthe24

haverageflow

ortemperaturerespon

setoETo

influence.Lag

ismaxim

umcorrelationintid

aldays

(td)

ordays

(d)from

Fig.9.Ind

icated

as“N

S”whenno

tsign

ificant

Driverinfluence

RMStid

einflu

ence

Lag

(td)

Dielmeteorology

(ETo)influ

ence

Lag

(d)

Geomorph

icinteraction

Com

ment

Residualflow

respon

seUpto

2cm

upstream

directionforseveral

days.Geomorph

iclin

k

−1

Weakcomparedto

tideinfluence

NS

Hightid

esexceed

slou

ghbank

height.Slow

surface

andhy

porheicdrainage

(Fig.1)

Stron

ggeom

orph

icmediatio

nat

elevationthresholdnear

MHHW

generatesfloo

ddo

minance.Overbank

flow

leads(lag

-1)peak

tidestreng

th(Fig.3,A;F

ig.9,S1)

becausetid

eelevationexceeds

marsh

plainelevationin

days

priorto

RMStid

eheight

maxim

um.

Tide/geom

orph

olog

yinfluencedo

minates

EToinfluence

FM

Spring

residu

alflow

Upto

0.8cm

lagg

edrespon

seto

spring

tiderelaxatio

n

3Weakcomparedto

tideinfluence

NS

Sim

pleland

–water

interface

onlevee(Fig.1)

Tidalresidu

alflow

respon

dsto

thechan

gein

RMStid

eheight

asz

meantid

eelevationrelaxesindays

afterspring

tidemaxim

um.S

Hflow

thereforelags

thepeak

RMStid

eheight

(Fig

9,S2).S

imilar

totheestuaryat

large,SH

isebbdominant.Weaklagged

inverse

correlationto

ETo

(Fig.10,S1)

FM

Neap

residu

alflow

0.2to

0.6cm

residu

alebbdirectionflow

−1

Tim

e-aligned.

Depends

onETo

magnitude

and

water

residence

time

0Marsh

plaindrainage

isslow

tolow-order

creeks

and

hypo

rheiczone

Com

plex

interactionof

threeprocesses.Heattransfer

processes(as

ETo

)candrivewater

advectionup

stream

viaevaporation/

evapotranspiratio

n(Fig

9,N5;

Fig

10,N1).Thisiscoun

teracted

bydegreesfrom

positiv

eadvectionviasurfaceandhy

porheic

drainage

ofprevious

spring

tidestoragein

concertwith

estuary

drainin

days

before

minim

umRMStid

eheight

Residual

Tem

perature

Respo

nse

SH

Neap

residu

alflow

0.1to

0.4cm

residu

alebbdirectionflow

−1

Tim

e-aligned.

Depends

onETo

magnitude

and

water

residence

time

0Sim

pleland

–water

interface

onlevee

Chang

ein

RMStid

eheight

(and

loweringmeantid

eelevation)

drives

lag−2,

−1,

0do

wnstream

tidal

averageflow

(Fig

9,N2).

Dielaverageflow

respon

dsim

mediately

(lag

0)to

channel

evaporation(asETo

)(Fig

9,N6).Essentially

noland

storage

contribu

tion

FM

Spring

residu

altemperature

Weaklagg

edeffect

NS

Persistent(∼5day)

influence.Tem

pflux

oscillates

with

lunarcycle.

Overallheat

sink

0Broad,shallow,multip

leday

water–atmosph

ereinterface

Residualtim

escale

integrates

variabletid

altim

escaleprocessesthat

depend

ontid

etim

ingandgeom

orph

icmediatio

n.Residual

temperature

isdo

minated

byETo

with

severaldaypersistence

possibly

from

marsh

plainstorageandslow

drain(Fig

9,S7).

Inversecorrelationto

GGRMShisasecond

aryinfluence(Fig

10,

S2).FM

isnetheat

sink

inwarm

mon

thsdu

ring

lunarmaxim

a(Fig

8,A)

SH

Spring

residu

altemperature

Weaklagg

edeffect

NS

Persistent(∼5day)

influence.Tem

p(heat)sink

with

irregu

larpattern

1Water–atmosph

ere

interactionlim

itedto

main

slou

ghchannel

Tem

perature

respon

seto

EToisrelatedto

residencetim

e(fun

ction

ofslou

ghpo

sitio

nandtid

alexcursionleng

th).Springtid

esexchange

warmer

slou

ghwater

with

distribu

tary

channelafter0–

4-daylag(Fig.9,

S8)

FM

Neap

residu

altemperature

Minim

al—

possible

lagg

edeffect

NS

Persistent/

throug

hout

neap

period

1Com

plex

interactionof

residencetim

eandtid

altrapping

Marsh

plaininteractionminim

ized

onweaktid

esallowingwarming

from

simultaneoushigh

waterresidencetim

eandwarmtemperature

insummer

(evenas

GGRMSh–Tempcorrelationisnotstatistically

significant).L

ocalslough

configurationprom

otes

tidaltrapping

and

along-slough

axistemposcillatio

n(Fig

4,B).Meteorology

influencepersiststhroughneap

tide(Fig.9,N3andN7)


slough length and tidal excursion as a function of positionalong the slough. Notwithstanding mixing, a given segmentof water could reside within a slough for hours or weeksdepending on tide strength. During neap tides, multiplealong-slough water temperature peaks, caused by tidal trap-ping, can be superimposed on the 24-h temperature patternwhen heated water segments are advected briefly out of theslough only to return on the next flood tide relativelyunmixed with the distributary channel (Fig. 4). In the low-order creeks of the natural slough, spring tides drive com-plete water exchange. During the transition from high–highto low–low tide, even the highest order slough exchangesmost of its volume. During lunar maxima, this transitionoccurs during early morning hours in the summer in recentdecades. Much of the high–high tide water is held inoverbank shallow storage at night where its temperature ismore sensitive to meteorological influence. We have notexplored the effect of this process on marsh plain produc-tivity (e.g., as chlorophyll a concentrations or as density ofaquatic and terrestrial invertebrates) but we suspect a localprimary production export subsidy could occur as a result ofshallow overbank retention and slow release (Enright et al.,unpublished material). The dynamics of this process willlikely change as the diel timing of marsh plain inundation byextreme tides slowly shifts within the 335-year cycle.

Additional confounding influences factor in. WhileRMS tide strength is a smooth process, overbank flowon the natural slough is a threshold event that step-changes the tidal and residual flow and temperaturepattern. We partitioned tidal strength by coarsely divid-ing the continuum RMS tide height data into spring andneap categories. Each of these factors presents a chal-lenge for untying driver influences and ecologicalimplications.

Leads and Lags Figure 4 shows how FM flow leads themaximum RMS tide because flood dominant currents appear assoon as thewaxing tide exceeds natural bank heights—generally1–3 days ahead of the lunar maximum. By the time tide heightspeak during the lunar maxima, the marsh plain has been floodedand drained possibly multiple times filling low depressions andthe field capacity of the soil. Similarly, because we monitoredtemperature at the slough mouths, observations integrate severalprocesses that impart a lag in the temperature response due to theheat capacity of water, the timing of sun and tides,hydrogeomorphic storage, and transport time to the sensors.Under both spring and neap tide conditions, water temperaturelags ETo by 1–2 days. The temperature response mixes outquickly during spring tides but persists for several days duringneap tides.

Feedbacks and Thresholds in High-Frequency Flow andTemperature Response The distribution of tidal currents isT

able

3(con

tinued)

Driverinfluence

RMStid

einflu

ence

Lag

(td)

Dielmeteorology

(ETo)influ

ence

Lag

(d)

Geomorph

icinteraction

Com

ment

SH

Neap

residu

altemperature

Minim

al—

possible

lagg

edeffect

NS

Persistent

throug

hout

neap

period

3Sloug

hleng

thandlim

ited

tidal

excursionretains

water

andallowswarming

GGRMSh–

Tem

perature

correlationisno

tsign

ificant.Nevertheless,

webelieve

weaktid

eisanecessarycond

ition

that

supp

ortsthe

ETo

–tempcorrelations

byincreasing

slou

ghresidencetim

e.Tem

perature

effect

ofmeteorology

persiststhroug

hneap

tide

(Fig.9,

N4andN8)


different between the sloughs despite equal forcing by tidesand meteorology. The maximum flood tide velocity of FMcurrents is near −0.4 ms−1 while the ebb tide duration isslightly longer and current maximums are no greater than0.24 ms−1. This asymmetry tends to transport sedimentupstream and indeed is a key process that sustains naturaltidal marsh elevations in the face of sea-level rise (e.g.,Temmerman et al. 2005). Maximum SH ebb and floodcurrents are nearly equal at approximately ±0.3 ms−1. Thisdifference in ebb-flood current dominance likely accountsfor the higher percentage of tidal prism-to-slough volume atFM compared to SH. Flood dominance on natural sloughs isa hydrogeomorphic process feedback that at once transportssediment overbank on high tides, decants it near the channeledge, and builds the very geomorphic threshold that causesflood dominance. As Fig. 5 shows, high-frequency flow–depth and flow–temperature relationships between sloughsare similar most of the time. Only when tide height exceedsnatural bank-full height do step-changes in residual flowand temperature responses appear. Compared to the modi-fied slough, the natural slough experiences a fortnightthreshold disturbance with consequences for subtidal time-scale heat transfer and water flux.

Residual Flow and Temperature Response At the tidal time-scale, flows are primarily driven by tides while temperatureis primarily driven by solar insolation. Tidal and diel re-siduals reveal more complex driver interactions. In the nat-ural slough (FM), residual flow and temperature is driven byinteraction between diel tide timing, tide height, degree ofwater exchange each tide, and slough morphology. Theresponse is complex because factors interact through feed-backs (residual currents affect water exchange, which af-fects evaporation, which affects residual currents),thresholds (tide height and currents step-change at bank-full height), non-linearity (temperature dynamics), and phas-ing harmonics (tide and solar maxima precess about12 °C/day). The modified slough response is less complex.Residual flow at SH responds weakly to tide strength inconcert with the greater estuary pattern because levees pre-vent overbank threshold hydroperiod responses. Evapora-tion can drive upstream residual currents during neap tideswhen air temperature, residence time, and water temperatureis high. During neap tides, the temperature response issimilar between sloughs when morphology differences areminimized.

Sensitivity to Comparison Timescales We also found thatthe temporal scale used to compare sloughs reveals differ-ences in morphology (Table 1). Comparing sloughs at thediel timescale, temperature averages and CDF’s are notsignificantly different regardless of fortnight tide status.When the averaging period is only 3 % longer (nominally

24 h versus 24.84 h), all water temperature and flow meansand CDF’s become significantly different. Tidal forcing, asmediated by geomorphology, dominates residual flow andtemperature at the tidal time scale on the natural slough(FM). The modified slough (SH) is disconnected from itsmarsh plain precluding the combined effect of tide strengthand meteorology to produce flow and temperature variability.

Temperature Regulation in the Estuary A key finding of thisstudy is that both sloughs were overall heat sinks during thestudy period. The average heat flux at FM is −5.8 C m3/s;the average heat flux at SH is −4.8 C m3/s (Fig. 8). FMexhibits tight coupling with the lunar status and tidestrength. Temperature outwelling occurs regularly on neaptides when average water elevation in the estuary declines.Spring tide temperature flux at FM responds strongly to tidestrength. Full moon RMS tide strength increases into Julywhen the strongest tides occur and overbank flow andstorage is greatest. As described above, high summer tidesflood the marsh plain in the late evening allowing latent,sensible, and long-wave heat transfer to the atmospherefrom water shallowly stored through the night when condi-tions are cool and often windy. Figure 8 illustrates thisprocess as tidally averaged heat flux but the primary driversare the interaction of high-frequency tide timing with mete-orological factors and slough morphology. Advection is thedominant heat flux transport process at FM during bothspring and neap tides though the mechanisms differ. Springtides allow water levels to exceed bank-full height whenchannel conveyance suddenly expands and accommodateslarge advective water and heat fluxes upstream. Neap tidedownstream advection at FM is the superposition ofdiminishing mean estuary water level and the release ofwater from marsh plain storage by overland, tidal creek,and hyporheic flows. Heat flux at SH is more irregular.The peak neap tide usually fluxes heat downstream forabout 2 days unless it coincides with high ETo when evap-oration and evapotranspiration can drive residual flow up-stream in opposition to estuarine drainage (e.g., compareFig. 3 and Fig. 8 ∼April 27).

Pulsed Inwelling and Outwelling The estuarine outwellinghypothesis (focused primarily on detritus and phytoplank-ton) has been debated since it emerged from classic papersby Teal (1962) and Odum (1968). Nixon (1980) notablyquestioned the generality of the hypothesis and Odum(2002) suggests that outwelling is better characterized as apulse phenomenon driven primarily by tides. Our studydemonstrates that tidal sloughs both outwell and inwelltemperature at tidal and lunar timescales. During neap tidesthe natural and modified sloughs regularly outwell heatthough the modified slough can “inwell” heat if ETo is highand advection by evaporation and evapotranspiration


overcomes residual slough outflows. The natural slough(FM) exhibits strong water influx over 8–9 days aroundthe full moon spring tide while accumulation is nearly flatfor the intervening three weeks (Fig. 3). When tides overtopslough banks, Fig. 8 shows that FM strongly absorbs heatfrom the near region. The modified slough (SH) generallyimports temperature in a more muted and irregular patternunless ETo is low on neap tides. Overall, both sloughs aretemperature sinks (inwell) with the natural slough moreefficiently importing heat. This pattern would likely changeif high spring tides occurred during day rather than night asthey will 16 decades hence.

Broad Timescale Temperature Dependence A novel findingof this study is that tidal and residual slough temperaturetransport depends on the diel and seasonal timing of highspring tides. As discussed above, there is a 335-year cycle inthe diel and seasonal timing of semi-diurnal high tideswhich precesses slightly more than one day per year(Malamud-Roam 2000). In recent and coming decades, highsummer spring tides in SuisunMarsh occur in the late eveningto early morning hours allowing natural sloughs to store watershallowly on broad marsh plains when the atmosphere iscooler than the water temperature. This is therefore a tidaltimescale outcome that depends profoundly on a century-scale astronomical process. Several drivers and processes atintermediate timescales also intervene. Figure 11 shows aconceptual model of natural tidal slough water temperature

dependence on interacting driver and process timescales. Thepurpose of the chart is to illustrate the breadth of timescalevariability among interacting processes that influence tidal-to-seasonal timescale slough water temperature. Temperaturevariability reflects a complex superposition of tide, weather,and climate driver frequencies mediated by morphology. Theconceptual model shows how tidal marsh slough flow andtemperature is ultimately a complex emergent phenomenaforced by unrelated drivers and intermediate outcomes atdisparate timescales.

Ecological Implications Diel timing of extreme tides hasimplications for ecological processes. Suisun Marsh current-ly experiences high spring tides near midnight in the sum-mer, and near noon in winter. Over the next 167 years, thispattern will switch. For now, mudflats are dewatered duringsummer days with implications for biochemical processrates, soil community metabolism, and availability of organ-isms to shorebirds. Tidal marshes today are inundated dur-ing the day in winter—perhaps somewhat before nektonearly life stages can fully access and utilize primary-secondary production. High marsh plain production in thelate spring and summer is out-welled on maximum ebb tidecurrents at night making it less available to visual foragers(Simenstad et al. 2000). Three to five decades hence, day-time high tides will occur in late winter and early springwhen nekton access and utilization may be improved. Othertidal marsh functions may also slowly shift through the 335-

Hours Days Months Years Decades Centuries

Drivers

Geomorph-ology& physical

outcomeinteractions

ProcessLinkages

EmergentAbiotic and

Biotic Functions

Driver influenceProcess influenceFeedback

Astronomical

Meteorology/climate

Timescale of variability

Inter-timescale astronomical and climatedriver interactions

Air-land-water heat transfer processes

biological/ecological processes and functions

PDO

-- Tidal slough water temperature -- Tidal marsh morphology

Spring-neap tide

Season tide

335 year spring-neap tide precessionSeasonal extremes

climate

Marsh plain hydroperiod

Erosion/sedimentation

Diel solar insolation

Vegetation, SAV, benthic algae

Water temp

dispersion

Watertemp

advection

Watershed inflow

Mudflat/marsh plain exposure to sun and climate

Tidal height and current magnitude

semi-diurnal

tideMeteorology

ENSO

Diel timing of tide height and currents

Ratio tidal excursion/slough length

Fig. 11 Conceptual model ofnatural tidal slough watertemperature dependence oninteracting driver and processtimescales. Box width indicatesbreadth of timescale variability.Ultimate slough watertemperature outcome shown ingray


year cycle. For example, within their capacity, nekton ac-commodates salinity, temperature, forage, and refugechanges within the compressed spatial gradients of tidalmarshes. Adaptations to periodic physical processes likethe regular availability of cold water at predictable timescould be used to competitive advantage and may constitutea selection driver. In addition, the timing of the tidal cur-rents relative to the photo period also has implications forlong-term trends deduced from monitoring program data.For example, inferences regarding organisms whose be-havior is affected by photo period but whose transport andposition in the estuary are affected by the tidal currentsmay be biased unless the timing between day/night andthe tidal cycle is taken into account (Lucas et al. 2006;Burau and Bennett, in prep). Lastly, longer-term tidalprocesses and the importance of long-residence waterdeposited on the high marsh in ponds or in near-surfacesoil horizons have yet to be fully described. Given thatmost estuary tidal marsh plains hydrogeomorphically reg-ulate bank heights to mean high tide elevations where thehigher spring tides flow over bank, we propose this is acritical feature of geomorphic–biologic linkages thatmakes tidal landscapes so important in the ecology ofthe estuary at large. Large-scale loss of these landscapeshas been correlated with general declines of estuarinespecies, but few formal causal mechanisms of the sortdiscussed here have been demonstrated. We think it likelythat the spring tide shallow water storage on natural marshplains would host enhanced primary and secondary pro-duction during the “inter-spring” tide sequence. As this“aged” water drains back into high order sloughs follow-ing its residence on the marsh plain, the algal and inver-tebrate species it contains can be transported to andsubsidize heterotrophic habitats in the broader estuary(e.g. Cloern 2007). Should this indeed be the case, it isa simple matter to understand how recovering geomorphicpatterns to historic proportions might be a desired out-come of tidal marsh restoration in estuaries.

Summary Conclusions

We observed neighboring tidal sloughs with contrastingmorphologies and therefore contrasting water surfaceexposure to solar insolation and heat exchange process-es. The natural tidal marsh has elevation discontinuitieswhich produce tidal flow asymmetries and step-changesin hydroperiod. In turn, these intermediate drivers inter-mittently increase water exposure to air temperature andsolar insolation. Meteorological exposure in naturalmarshes is modulated by phasing of tidal dynamics athourly, lunar, seasonal, and decadal, and centennialtimescales.

& The natural slough (FM) exhibits comparatively strongflood dominant tidal currents on spring tides due togeomorphic controls. This process likely encouragessediment accretion and vegetation feedbacks therebystrengthening geomorphic control. The modified slough(SH) is ebb dominant similar to the greater estuarypattern. During the warm season, residual flow in themodified slough is driven constantly by meteorology,while residual flow in the natural slough oscillates be-tween meteorological control during neap tides andmorphology-tide interaction control during spring tides.

& At the tidal timescale, flows are strongly driven by tidalharmonic forcing while slough temperatures in thesloughs are driven by daily solar insolation and meteo-rological conditions. For subtidal timescales (greaterthan ∼1 day), slough flows and temperatures are drivenby complex and shifting interactions between heat trans-fer mechanisms and tide-morphology interactions.

& Both sloughs exhibit overall negative (upstream direct-ed) water flux in warm months due to evaporation andtranspiration, though the interaction mechanisms andpattern differ. In turn, both sloughs are net temperaturesinks primarily by advective transport with residual waterflow. FM temperature advection and dispersion are coherentwith lunar cycle tidal forcing and its morphology linkage toevaporation and transpiration. SH temperature advection isirregular and lower magnitude.

& Because we monitored temperature and flow at theslough mouths, measurements integrate several process-es that lead or lag the temporal pattern of driver energy.FM residual flow leads the maximum RMS tide becauseflood dominant currents appear as soon as waxing tidesexceed the natural bank height—generally 1–3 daysahead of the lunar maximum. Residual temperatureresponse generally lags drivers due to the heat capacity ofwater, geomorphic storage, transport time to the sensors,and the status of the 335-year precession of the diel timingof extreme tides.

& Phasing of a 335-year precession of diel timing of tidalextremes exerts a profound tidal and fortnight coolingeffect on both sloughs and the estuary at large. Morpho-logical mediation intensifies the effect on the naturalslough.

& Driver interactions in the modified slough are uncoupledby the complete disconnection of slough water from theformer marsh plain by levees.

& Tidal slough residual flow and temperature are an emergentresponse of a cascade of processes that are mediated bymorphology. Untangling driver influences is not straight-forward. The drivers we used can act together to influenceresidual flow or temperature, or they can act in oppositedirections with the outcome reflecting subtle changes inrelative strength of each driver.


& High-frequency water temperature regulation appears tobe a key function of natural tidal sloughs and dependscritically on geomorphic mediation. Natural tidal marshmorphology links tidal forcing to broad timescale watertemperature control. This work demonstrates how high-frequency current and water temperature variabilityemerges from multiple timescale interactions betweentidal harmonics, tidal marsh morphology, and solarinsolation.

& We see no reason to believe that these finding should notbroadly hold for tidal marshes in other estuaries. Thecooling function of natural tidal sloughs is an importantecosystem service and a likely species selection driver.Tidal marsh restoration efforts that return historical cur-rent and temperature patterns may improve competitiveadvantage and resilience of native species in the face ofcontemporary estuarine system stressors.

The levees of the modified slough disconnect not onlywater from land, but also water from atmospheric interac-tion. The severed land–water interactions profoundlychange current and water temperature dynamics. The north-ern reach of the San Francisco estuary contains hundreds ofmodified or disconnected terminal tidal sloughs where thecurrent and temperature regime is probably considerablychanged. A proper characterization of the change wouldrequire sophisticated modeling. In contrast, historical tidalmarshes were driven by interaction of meteorology, tide, andriver inputs and shaped by sedimentation—vegetation feed-backs. The key linking process is hydroperiod mediation bymorphology.

Based on our results, we speculate that pre-developmentcurrents and temperature regimes in the San Francisco Es-tuary were significantly influenced by tidal hydroperiodinteraction with natural tidal marsh morphology. Strongtemperature gradients and periodic low temperature refugiawould be produced in a regular pattern in tidal marsh creeks.Native species may have evolved adaptations to the pattern.The 335-year cycle of diel tidal extreme timing assures thatshallow hydroperiod dynamics on tidal marsh plains willcoincide with mid-day solar insolation in the next centurywhich will likely produce higher temperatures. Other estu-arine components like mudflats are also sensitive to the dielhigh tide timing cycle. Today, mudflats are generally moreexposed to solar insolation in summer with consequencesfor a cascade of outcomes like soil metabolism and wadingbird foraging. These outcomes may express very differentlythe next century.

Acknowledgments Thanks to two anonymous reviewers forcomments that improved the paper. One reviewer in particular exem-plified the spirit of scientific peer review by offering an extremelycareful and thoughtful appraisal which greatly clarified the manuscript.We are humbled and honored by the depth of consideration. Thanks to

Curt Battenfeld, Angelo Garcia and Randy Smith for capable fieldassistance. Thanks to the Interagency Ecological Program for bridgefunding.

Open Access This article is distributed under the terms of the CreativeCommons Attribution License which permits any use, distribution, andreproduction in any medium, provided the original author(s) and thesource are credited.

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