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Jon R. Burau

Publications and source records attributed to Jon R. Burau.

35 records · Page 2Linked to original sources
USGS2013

Broad timescale forcing and geomorphic mediation of tidal marsh flow and temperature dynamics

Tidal marsh functions are driven by interactions between tides, landscape morphology, and emergent vegetation. Less often considered are the diurnal pattern of tide extremes and seasonal variation of solar insolation in the mix of tidal marsh driver interactions. This work demonstrates how high-frequency hydroperiod and water temperature variability emerges from disparate timescale interactions between tidal marsh morphology, tidal harmonics, and meteorology in the San Francisco Estuary. We compare the tidal and residual flow and temperature response of neighboring tidal sloughs, one possessing natural tidal marsh morphology, and one that is modified for water control. We show that the natural tidal marsh is tuned to lunar phase and produces tidal and fortnight water temperature variability through interacting tide, meteorology, and geomorphic linkages. In contrast, temperature variability is dampened in the modified slough where overbank marsh plain connection is severed by levees. Despite geomorphic differences, a key finding is that both sloughs are heat sinks in summer by latent heat flux-driven residual upstream water advection and sensible and long-wave heat transfer. The precession of a 335-year tidal harmonic assures that these dynamics will shift in the future. Water temperature regulation appears to be a key function of natural tidal sloughs that depends critically on geomorphic mediation. We investigate approaches to untangling the relative influence of sun versus tide on residual water and temperature transport as a function of system morphology. The findings of this study likely have ecological consequences and suggest physical process metrics for tidal marsh restoration performance.

California↗
USGS2013

The Regional Salmon Outmigration Study--survival and migration routing of juvenile Chinook salmon in the Sacramento-San Joaquin River Delta during the winter of 2008-09

Juvenile Chinook salmon (Oncorhynchus tshawytscha) emigrating from natal tributaries of the Sacramento River may use a number of migration routes to navigate the Sacramento-San Joaquin River Delta (hereafter called “the Delta”), each of which may influence their probability of surviving. We applied a mark-recapture model to data from acoustically tagged juvenile late fall-run Chinook salmon that migrated through the Delta during the winter of 2008–09 to estimate route entrainment, survival, and migration times through the Delta. A tag-life study was conducted to determine the potential for premature tag failure. Tag failure began after 12 days and continued until the 45th day. Travel times of tagged fish exceeded minimum tag-failure times, indicating that survival estimates obtained from this study were negatively biased due to tag failure prior to fish exiting the Delta. Survival estimates were not adjusted and represent the joint probability of tag survival and fish survival. However, relative comparisons of survival among Chinook salmon choosing different routes appeared to be robust to tag failure, and migration-routing parameters were unaffected by tag failure. Migration-routing patterns were consistent among release groups. The Sacramento River was the primary migration route for all release groups except one. The percentage of fish entering the Sacramento River ranged from 33 to 55 percent. Sutter and Steamboat Sloughs were the secondary migration route for 9 of the 10 releases. The percentage of fish migrating through this route ranged from 10 to 35 percent. Entrainment into the interior Delta ranged from 15 to 33 percent. The Delta Cross Channel gates were open for 7 of the 10 releases. Entrainment into the interior Delta through the cross channel ranged from 1 to 27 percent. We estimated route-specific survival for 10 release groups that were released between November 14, 2008, and January 19, 2009. Population-level survival through the Delta (S Delta ) ranged from 0.019 (standard error of 0.012) to 0.277 (standard error of 0.041) among releases, which represent the probability of a fish surviving from Sacramento to Chipps Island with an operational transmitter. Sacramento River flows throughout the study period were approximately 8,000–15,000 cubic feet per second at Freeport, suggesting that variability in flow contributed little to differences in survival between releases. Fish migrating through the Sacramento River had the highest survival for most releases. Survival in Sutter and Steamboat Sloughs was slightly lower than survival in the Sacramento River for 7 of the 10 releases, but higher than survival in the Sacramento River for 3 releases. Survival in the interior Delta was lowest for all release groups except for one release in November. With the exception of this November release, survival patterns across release groups were similar to those of previous studies.

California↗
USGS2012

2011 Georgiana Slough non-physical barrier performance evaluation project report

The Sacramento River and its tributaries support populations of anadromous fish species including winter-run, spring-run, fall-run, and late fall–run Chinook salmon ( Oncorhynchus tshawytscha ); and steelhead ( O. mykiss ). Several of these species are listed as threatened or endangered under the California Endangered Species Act (CESA), federal Endangered Species Act (ESA), or both. These species spawn and rear in Sacramento River tributaries; adults use the mainstem Sacramento River for primarily upstream migration and juveniles use it for downstream migration. Juvenile Chinook salmon and steelhead migrate through the lower river during winter and spring. During their downstream migration, juvenile salmonids encounter alternative pathways, such as Sutter and Steamboat Sloughs, the Sacramento–San Joaquin Delta (Delta), Delta Cross Channel (DCC), and Georgiana Slough. Likewise, sturgeon juveniles migrate downstream in the Sacramento River basin to the Delta, utilizing the distributary channels to rear within and migrate through the system. Georgiana Slough is a natural channel that allows water and fish to move into the interior Delta. Previous studies have demonstrated that juvenile Chinook salmon experience greater mortality when migrating into Georgiana Slough than those juveniles that continue to migrate downstream in the Sacramento River (Perry 2010). Movement and/or diversion of these fish into the interior and south Delta increases the likelihood of losses through predation, entrainment into non-project Delta diversions, and mortality associated with the State Water Project (SWP) and Central Valley Project (CVP) pumping facilities in the south Delta (Perry 2010; NMFS 2009). Figure ES-1 shows the migration pathways in the lower Sacramento River and Delta for outmigrating anadromous salmonids, and the location of the DCC, and the SWP and CVP pumping facilities in the south Delta. Passage of juvenile salmonids from the Sacramento River into the interior Delta through the DCC can be reduced through seasonal closure of the radial gates (February through May); however, no similar protection is available to reduce the movement of juvenile salmonids from the Sacramento River into the interior Delta through Georgiana Slough. Flows into Georgiana Slough improve water quality and flushing in the interior Delta and free access encourages use by recreational boaters. Because of these benefits, alternatives to the installation of a physical barrier (i.e. radial gates), are being investigated. Under the ESA, the National Marine Fisheries Service (NMFS) issued the 2009 Biological and Conference Opinion for the Long‐Term Operations of the Central Valley Project and State Water Project (BO) for Chinook salmon and other listed anadromous fish species (NMFS 2009). Reasonable and Prudent Alternative (RPA) Action IV.1.3 of the BO requires the California Department of Water Resources (DWR) and the U.S. Bureau of Reclamation (Reclamation) to consider engineering solutions to reduce the diversion of juvenile salmonids from the Sacramento River into the interior and south Delta. DWR implemented the 2011 Georgiana Slough NonPhysical Barrier (GSNPB) Study to test the effectiveness of using a non-physical barrier, referred to as a behavioral Bio-Acoustic Fish Fence (BAFF), that combines three stimuli to deter juvenile Chinook salmon from entering Georgiana Slough: sound, high-intensity modulated light (previously known as stroboscopic light), and a bubble curtain. This report presents the results of the experimental tests conducted in 2011.

California↗
USGS2008

Dual-RiverSonde measurements of two-dimensional river flow patterns

Two-dimensional river flow patterns have been measured using a pair of RiverSondes in two experiments in the Sacramento-San Joaquin River Delta system of central California during April and October 2007. An experiment was conducted at Walnut Grove, California in order to explore the use of dual RiverSondes to measure flow patterns at a location which is important in the study of juvenile fish migration. The data available during the first experiment were limited by low wind, so a second experiment was conducted at Threemile Slough where wind conditions and surface turbulence historically have resulted in abundant data. Both experiments included ADCP near-surface velocity measurements from either manned or unmanned boats. Both experiments showed good comparisons between the RiverSonde and ADCP measurements. The flow conditions at both locations are dominated by tidal effects, with partial flow reversal at Walnut Grove and complete flow reversal at Threemile Slough. Both systems showed complex flow patterns during the flow reversals. Quantitative comparisons between the RiverSondes and an ADCP on a manned boat at Walnut Grove showed mean differences of 4.5 cm/s in the u (eastward) and 7.6 cm/s in the v (northward) components, and RMS differences of 14.7 cm/s in the u component and 21.0 cm/s in the v component. Quantitative comparisons between the RiverSondes and ADCPs on autonomous survey vessels at Threemile Slough showed mean differences of 0.007 cm/s in the u component and 0.5 cm/s in the v component, and RMS differences of 7.9 cm/s in the u component and 13.5 cm/s in the v component after obvious outliers were removed. ?? 2008 IEEE.

Conference Paper↗
USGS2007

Effects of flow diversions on water and habitat quality: Examples from California's highly manipulated Sacramento–San Joaquin Delta

We use selected monitoring data to illustrate how localized water diversions from seasonal barriers, gate operations, and export pumps alter water quality across the Sacramento-San Joaquin Delta (California). Dynamics of water-quality variability are complex because the Delta is a mixing zone of water from the Sacramento and San Joaquin Rivers, agricultural return water, and the San Francisco Estuary. Each source has distinct water-quality characteristics, and the contribution of each source varies in response to natural hydrologic variability and water diversions. We use simulations with a tidal hydrodynamic model to reveal how three diversion events, as case studies, influence water quality through their alteration of Delta-wide water circulation patterns and flushing time. Reduction of export pumping decreases the proportion of Sacramento- to San Joaquin-derived fresh water in the central Delta, leading to rapid increases in salinity. Delta Cross Channel gate operations control salinity in the western Delta and alter the freshwater source distribution in the central Delta. Removal of the head of Old River barrier, in autumn, increases the flushing time of the Stockton Ship Channel from days to weeks, contributing to a depletion of dissolved oxygen. Each shift in water quality has implications either for habitat quality or municipal drinking water, illustrating the importance of a systems view to anticipate the suite of changes induced by flow manipulations, and to minimize the conflicts inherent in allocations of scarce resources to meet multiple objectives.

California↗
USGS2006

Flow convergence caused by a salinity minimum in a tidal channel

Residence times of dissolved substances and sedimentation rates in tidal channels are affected by residual (tidally averaged) circulation patterns. One influence on these circulation patterns is the longitudinal density gradient. In most estuaries the longitudinal density gradient typically maintains a constant direction. However, a junction of tidal channels can create a local reversal (change in sign) of the density gradient. This can occur due to a difference in the phase of tidal currents in each channel. In San Francisco Bay, the phasing of the currents at the junction of Mare Island Strait and Carquinez Strait produces a local salinity minimum in Mare Island Strait. At the location of a local salinity minimum the longitudinal density gradient reverses direction. This paper presents four numerical models that were used to investigate the circulation caused by the salinity minimum: (1) A simple one-dimensional (1D) finite difference model demonstrates that a local salinity minimum is advected into Mare Island Strait from the junction with Carquinez Strait during flood tide. (2) A three-dimensional (3D) hydrodynamic finite element model is used to compute the tidally averaged circulation in a channel that contains a salinity minimum (a change in the sign of the longitudinal density gradient) and compares that to a channel that contains a longitudinal density gradient in a constant direction. The tidally averaged circulation produced by the salinity minimum is characterized by converging flow at the bed and diverging flow at the surface, whereas the circulation produced by the constant direction gradient is characterized by converging flow at the bed and downstream surface currents. These velocity fields are used to drive both a particle tracking and a sediment transport model. (3) A particle tracking model demonstrates a 30 percent increase in the residence time of neutrally buoyant particles transported through the salinity minimum, as compared to transport through a constant direction density gradient. (4) A sediment transport model demonstrates increased deposition at the near-bed null point of the salinity minimum, as compared to the constant direction gradient null point. These results are corroborated by historically noted large sedimentation rates and a local maximum of selenium accumulation in clams at the null point in Mare Island Strait.

California↗
USGS2002

Plasticity in vertical migration by native and exotic estuarine fishes in a dynamic low‐salinity zone

We investigated the degree of flexibility in retention strategies of young fishes in the low‐salinity zone (LSZ) of the San Francisco Estuary during years of highly variable river flow. We conducted depth‐stratified sampling over three full tidal cycles in each year from 1994 to 1996. In 1994, exotic striped bass ( Morone saxatilis ), native longfin smelt ( Spirinchus thaleichthys ), and exotic yellowfin goby ( Acanthogobus flavimanus ) migrated tidally, occurring near the surface on flood tides and near the bottom on ebb tides. This strategy may have facilitated retention, because landward residual currents were absent in this drought year. During 1995, this behavior persisted for striped bass and yellowfin goby, even though landward residual currents were present under high river‐flow conditions. In moderate river‐flow conditions (1996), longfin smelt again migrated tidally, whereas at another station adjacent to shallow bays, longfin smelt, striped bass, and native delta smelt (Hypomesus transpacificus) migrated on a reverse diel cycle, occurring near the surface by day and at depth by night. Reverse diel migration may facilitate horizontal transport and retention. Therefore, young fishes appeared to be behaviorally flexible in different environmental conditions to maximize retention. Vertical migrations may also enhance feeding success because zooplankton prey similarly migrated in the LSZ. Our study underscores the value of interdisciplinary studies in a variety of environmental conditions to decipher the range of organism behaviors promoting transport and retention in optimal habitats.

California↗
USGS2002

Persistence of tidally-oriented vertical migration by zooplankton in a temperate estuary

Tidal vertical migration by zooplankton is a common phenomenon in estuaries, usually associated with landward movement of meroplankton or position maintenance of holoplankton. Little is known about the persistence of this behavior, its spatial variability, or its response to changing environmental conditions. We extended a previous study of tidal movements of zooplankton in the low-salinity zone (LSZ) of the San Francisco estuary in 1994 to include data from two additional years with very different hydrology. Freshwater flow during sampling in 1995 was about 7-fold greater than in 1994; the LSZ was about 28 km further seaward, and gravitational circulation in the LSZ was strong. In 1996 freshwater flow and LSZ position were intermediate but, because the LSZ was in shallower water in 1996 than in 1995, gravitational circulation was uncommon. Behavior of copepods in both years was similar to that reported in 1994 with some tidal migration observed during most cruises. An exception was the introduced carnivorous copepod Tortanus dextrilobatus , which did not migrate and maintained a position deep in the water column (1995 only). In 1996, mysids mainly stayed near the bottom with evidence for vertical migration from only 1 of 6 data sets, whereas amphipods migrated slightly on a diel schedule; these behaviors contrasted with the tidal migration observed in 1994. The bay shrimp Crangon franciscorum did not appear to migrate, but was more abundant in the water column during both ebb and flood, suggesting passive vertical dispersal. Zooplankton did not appear to maintain position by interactions with lateral circulation cells. The results for copepods suggest rigidity in behavior with little or no relaxation of the vertical movement in 1995 when strong gravitational circulation would have made upstream movement relatively easy. Mysids and amphipods altered their behavior depending on local conditions related to freshwater flow.

California↗
USGS2002

Structure and flow-induced variability of the subtidal salinity field in northern San Francisco Bay

The structure of the salinity field in northern San Francisco Bay and how it is affected by freshwater flow are discussed. Two datasets are examined: the first is 23 years of daily salinity data taken by the U.S. Bureau of Reclamation along the axis of northern San Francisco Bay; the second is a set of salinity transects taken by the U.S. Geological Survey between 1988 and 1993. Central to this paper is a measure of salinity intrusion, X 2 : the distance from the Golden Gate Bridge to where the bottom salinity is 2 psu. Using X 2 to scale distance, the authors find that for most flow conditions, the mean salinity distribution of the estuary is nearly self-similar with a salinity gradient in the center 70% of the region between the Golden Gate and X 2 that is proportional to X −1 2 . Analysis of covariability of Q and X 2 showed a characteristic timescale of adjustment of the salinity field of approximately 2 weeks. The steady-state response deduced from the X 2 time series implies that X 2 is proportional to riverflow to the 1/7 power. This relation, which differs from the standard 1/3 power dependence that is derived theoretically assuming constant exchange coefficients, shows that the upstream salt flux associated with gravitational circulation is more sensitive to the longitudinal salinity gradient than theory supposes. This is attributed to the strengthening of stratification caused by the stronger longitudinal salinity gradient that accompanies larger river flows.

California↗
USGS2002

Pulsey, patchy water quality in the delta: Implications for meaningful monitoring

Valuable water quality and biological datasets have been gathered in the Sacramento-San Joaquin Delta for decades, most notably by the Interagency Ecological Program’s Environmental Monitoring Program (EMP). These extensive data have provided a means of analyzing and detecting long-term trends in water quality and ecosystem function (Jassby and others 2002; Kimmerer and Orsi 1996; Orsi and Mecum 1996) and may shape future restoration actions in the region. EMP water quality data—as well as data generated by the San Francisco Estuary Institute’s (SFEI) Regional Monitoring Program (RMP) and research groups like our own—have often focused on single, monthly or seasonal samples taken at several discrete points in space. Although such discrete data often push the practical limits of our equipment and human resources, higher resolution monitoring approaches can reveal limitations (in some cases severe) of these more coarse sampling schemes.

Interagency Ecological Program Newsletter↗
USGS2001

Hydrodynamic and suspended-solids concentration measurements in Suisun Bay, California, 1995

Sea level, current velocity, water temperature, salinity (computed from conductivity and temperature), and suspended-solids data collected in Suisun Bay, California, from May 30, 1995, through October 27, 1995, by the U.S. Geological Survey are documented in this report. Data were collected concurrently at 21 sites. Various parameters were measured at each site. Velocity-profile data were collected at 6 sites, single-point velocity measurements were made at 9 sites, salinity data were collected at 20 sites, and suspended-solids concentrations were measured at 10 sites. Sea-level and velocity data are presented in three forms; harmonic analysis results; time-series plots (sea level, current speed, and current direction versus time); and time-series plots of low-pass-filtered time series. Temperature, salinity, and suspended-solids data are presented as plots of raw and low-pass-filtered time series.The velocity and salinity data presented in this report document a period when the residual current patterns and salt field were transitioning from a freshwater-inflow-dominated condition towards a quasi steady-state summer condition when density-driven circulation and tidal nonlinearities became relatively more important as long-term transport mechanisms. Sacramento-San Joaquin River Delta outflow was high prior to and during this study, so the tidally averaged salinities were abnormally low for this time of year. For example, the tidally averaged salinities varied from 0-12 at Martinez, the western border of Suisun Bay, to a maximum of 2 at Mallard Island, the eastern border of Suisun Bay. Even though salinities increased overall in Suisun Bay during the study period, the near-bed residual currents primarily were directed seaward. Therefore, salinity intrusion through Suisun Bay towards the Delta primarily was accomplished in the absence of the tidally averaged, two-layer flow known as gravitational circulation where, by definition, the net currents are landward at the bed. The Folsom Dam spillway gate failure on July 17, 1995, was analyzed to determine the effect on the hydrodynamics of Suisun Bay. The peak flow of the American River reached roughly 1,000 cubic meters per second as a result of the failure, which is relatively small. This was roughly 15 percent of the approximate 7,000 cubic meters per second tidal flows that occur daily in Suisun Bay and was likely attenuated greatly. Based on analysis of tidally averaged near-bed salinity and depth-averaged currents after the failure, the effect was essentially nonexistent and is indistinguishable from the natural variability.

Water-Resources Investigations Report↗
USGS2000

Recent research on the hydrodynamics of the Sacramento - San Joaquin River Delta and north San Francisco Bay

This article presents an overview of recent findings from hydrodynamic research on circulation and mixing in the Sacramento-San Joaquin Delta (Delta) (Figure 1) and North San Francisco Bay (North Bay) (Figure 2). For the purposes of this article, North Bay includes San Pablo Bay, Carquinez Strait, and Suisun Bay. The findings presented are those gained from field studies carried out by the U.S. Geological Survey (USGS), as part of the Interagency Ecological Program (IEP), and Stanford University beginning about 1993. The premise behind these studies was that a basic understanding of circulation and mixing patterns in the Bay and Delta is an essential part of understanding how biota and water quality are affected by natural hydrologic variability, water appropriation, and development activities. Data collected for the field studies described in this article have significantly improved our understanding of Bay and Delta hydrodynamics. Measured flows ,in the Delta have provided valuable information on how water moves through the Delta's network of channels and how export pumping affects flows. Studies of the shallows and shallow-channel exchange processes conducted in Honker Bay have shown that the water residence time in Honker Bay is much shorter than previously reported (on the order of hours to several tidal cycles instead ofweeks). Suisun Bay studies have provided data on hydrodynamic transport and accumulation mechanisms that operate primarily in the channels. The Suisun Bay studies have caused us to revise our understanding of residual circulation in the channels of North Bay and of "entrapment" mechanisms in the low salinity zone. Finally, detailed tidal and residual (tidally averaged) time-scale studies of the mechanisms that control gravitational circulation in the estuary show that density-driven transport in the channels is governed by turbulence time-scale (seconds) interactions between the mean flow and stratification. The hydrodynamic research summarized in this article spans a range of estuarine environments (deep water channels to shallow water habitats and brackish water to freshwater) at time scales that range from seconds to years.

California↗
USGS1998

Summary of findings about circulation and the estuarine turbidity maximum in Suisun Bay, California

Suisun Bay, California, is the most landward subembayment of San Francisco Bay (fig. 1) and is an important ecological habitat (Cloern and others, 1983; Jassby and others, 1995). During the 1960s and 1970s, data collected in Suisun Bay were analyzed to develop a conceptual model of how water, salt, and sediment move within and through the Bay. This conceptual model has been used to manage freshwater flows from the Sacramento-San Joaquin Delta to Suisun Bay to improve habitat for several threatened and endangered fish species. Instrumentation used to measure water velocity, salinity, and suspended-solids concentration (SSC) greatly improved during the 1980s and 1990s. The U.S. Geological Survey (USGS) has utilized these new instruments to collect one of the largest, high-quality hydrodynamic and sediment data sets available for any estuary. Analysis of these new data has led to the revision of the conceptual model of circulation and sediment transport in Suisun Bay.

Fact Sheet↗
USGS1997

Sediment transport pathway in the back of a nearly semienclosed subembayment of San Francisco Bay, California

Time series measurements of current velocity, depth and suspended-solids concentration (SSC) were used to obtain suspended-solids fluxes (SSF) during the fall at central Honker Bay and Spoonbill Creek. A wind-induced shear stress increases SSF out of Honker Bay through Spoonbill Creek by combining two effects: (1) wind-wave resuspension of bed sediments, and (2) wind shear raises the water level at the Honker Bay. High SSC water advected from Honker Bay into the Sacramento River does not return on the following ebb tide, which creates the dispersive SSF. The total SSF was always out of Honker Bay during the fall suggesting that high metals and pesticides concentrations are not caused by transport through Spoonbill Creek into Honker Bay.

California↗
USGS1996

Suspended-solids flux at a shallow-water site in south San Francisco Bay, California

Time series measurements of current velocity and suspended solids-concentration (SSC) made during December 1993 and March 1994 at a shallow-water site in South San Francisco Bay were used to estimate and compare suspended-solids flux during the two periods. In December, the average residual flux at the site was 2.88 g/m/s, to the northeast, whereas in March the average residual flux was four times greater, 12.2 g/m/s, and was directed to the southeast, the direction of flood tide. Residual flux was decomposed and the three components that accounted for most of the flux were analyzed: residual advective flux (Stokes drift flux ( u ' h ' c ), and dispersive flux, which is the tidal cycle correlation between velocity and SSC ( u ' h'c ). During both periods, the Stokes drift flux was to the north, and the dispersive flux was to the southeast. In December, these two components, with nearly opposite directions, had the greatest magnitudes, resulting in a lower total residual flux. In March, the residual advective flux was greater than the Stokes drift flux and was in the same direction as the dispersive flux because of a southeasterly residual current. Wind data indicate that the residual current in March was induced by persistent northwest winds. The southeasterly dispersive flux in March and December was due to generally higher SSC on flood than ebb tides. Increases in SSC frequently occurred at low water (before flood tides). Comparison of calculated bottom orbital velocities to SSC identified wind waves as a mechanism of resuspension.

Conference Paper↗
USGS1988

Predicting tidal currents in San Francisco Bay using a spectral model

This paper describes the formulation of a spectral (or frequency based) model which solves the linearized shallow water equations. To account for highly variable basin bathymetry, spectral solutions are obtained using the finite element method which allows the strategic placement of the computation points in the specific areas of interest or in areas where the gradients of the dependent variables are expected to be large. Model results are compared with data using simple statistics to judge overall model performance in the San Francisco Bay estuary. Once the model is calibrated and verified, prediction of the tides and tidal currents in San Francisco Bay is accomplished by applying astronomical tides (harmonic constants deduced from field data) at the prediction time along the model boundaries.

Conference Paper↗