Showing papers in "San Francisco Estuary and Watershed Science in 2008"
TL;DR: The main source of interannual phytoplankton variability in the Delta during 1996-2005, including the upward trend, appears to have been freshwater flow variability and its effect on particle residence time as discussed by the authors.
Abstract: Several pelagic fish populations in the upper San Francisco Estuary have recently declined to historically low abundances, prompting an interest in the status of their food supply. Previous studies have indicated that the primary food supply for metazoans in the Delta is phytoplankton productivity, and the long-term decrease in phytoplankton over the last few decades may very well play a role in the long-term decline of pelagic fish abundance. Regional phytoplankton biomass trends during 1996–2005, however, are positive in the Delta and neutral in Suisun Bay, the two major sub-regions of the upper estuary. The trend in Delta primary productivity is also positive. Changes in phytoplankton biomass and production during the last decade are therefore unlikely to be the cause of these more recent metazoan declines. The main source of interannual phytoplankton variability in the Delta during 1996–2005, including the upward trend, appears to have been freshwater flow variability and its effect on particle residence time. This conclusion is supported by trend analyses; the concurrence of these time trends at widely-separated stations; empirical models at the annual and monthly time scales; particle residence time estimates; and experience from other estuaries. A significant temperature increase was also noticed, at least partially independent of flow changes, but its net effect on the phytoplankton community is unknown because of differential effects on growth and loss processes. Phytoplankton biomass in Suisun Bay, in contrast to the Delta, did not increase during 1996–2005. Consistent with this observation, Suisun Bay phytoplankton exhibited relatively low responsiveness to flow variability. This behavior differs from earlier chlorophyll-flow relationships reported in the literature. The reason appears to be the invasion of Suisun Bay by a clam—Corbula amurensis—in 1986, which has since maintained the phytoplankton community mostly at low levels by vigorous filter-feeding. In the past, flows into Suisun Bay generally diluted the higher phytoplankton concentrations within the bay; now they bring in higher phytoplankton concentrations from upstream. The supply of phytoplankton carbon to Suisun Bay has always been dominated by allochthonous sources, at least for mean flow conditions. Now this dominance must be even more pronounced.
130 citations
TL;DR: In this paper, the proportional losses of Sacramento River Chinook salmon (Oncorhynchus tshawytscha) and delta smelt (Hypomesus transpacificus) were estimated based on recoveries of tagged smolts released in the upper Sacramento River basin and recovered at the fish-salvage facilities in the south Delta and in a trawling program in the western Delta.
Abstract: Pumping at the water export facilities in the southern Sacramento-San Joaquin Delta kills fish at and near the associated fish-salvage facilities. Correlative analyses of salvage counts with population indices have failed to provide quantitative estimates of the magnitude of this mortality. I estimated the proportional losses of Sacramento River Chinook salmon (Oncorhynchus tshawytscha) and delta smelt (Hypomesus transpacificus) to place these losses in a population context. The estimate for salmon was based on recoveries of tagged smolts released in the upper Sacramento River basin, and recovered at the fish-salvage facilities in the south Delta and in a trawling program in the western Delta. The proportion of fish salvaged increased with export flow, with a mean value around 10% at the highest export flows recorded. Mortality was around 10% if pre-salvage losses were about 80%, but this value is nearly unconstrained. Losses of adult delta smelt in winter and young delta smelt in spring were estimated from salvage data (adults) corrected for estimated presalvage survival, or from trawl data in the southern Delta (young). These losses were divided by population size and accumulated over the respective seasons. Losses of adult delta smelt were 1–50% (median 15%), although the highest value may have been biased upward. Daily losses of larvae and juveniles were 0–8%, and seasonal losses accumulated were 0–25% (median 13%). The effect of these losses on population abundance was obscured by subsequent 50-fold variability in survival from summer to fall.
117 citations
Journal Article•
TL;DR: A suite of studies that assessed responses of four taxonomic groups (insects, birds, bats, and rodents) were published in this paper, focusing on the success of riparian restoration projects.
Abstract: Studies that assess the success of riparian restoration projects seldom focus on wildlife. More generally, vegetation characteristics are studied, with the assumption that animal populations will recover once adequate habitats are established. On the Sacramento River, millions of dollars have been spent on habitat restoration, yet few studies of wildlife response have been published. Here we present the major findings of a suite of studies that assessed responses of four taxonomic groups (insects, birds, bats, and rodents). Study designs fell primarily into two broad categories: comparisons of restoration sites of different ages, and comparisons of restoration sites with agricultural and remnant riparian sites.
68 citations
TL;DR: The Delta Simulation Model-2 hydrodynamic model and its particle tracking model was used to examine the principal determinants of entrainment losses to the export facilities and how movement of fish through the Delta may be influenced by flow.
Abstract: Movements of pelagic organisms in the tidal freshwater regions of estuaries are sensitive to the movements of water. In the Sacramento-San Joaquin Delta—the tidal freshwater reach of the San Francisco Estuary—such movements are key to losses of fish and other organisms to entrainment in large waterexport facilities. We used the Delta Simulation Model-2 hydrodynamic model and its particle tracking model to examine the principal determinants of entrainment losses to the export facilities and how movement of fish through the Delta may be influenced by flow. We modeled 936 scenarios for 74 different conditions of flow, diversions, tides, and removable barriers to address seven questions regarding hydrodynamics and entrainment risk in the Delta. Tide had relatively small effects on fate and residence time of particles. Release location and hydrology interacted to control particle fate and residence time. The ratio of flow into the export facilities to freshwater flow into the Delta (export:inflow or EI ratio) was a useful predictor of entrainment probability if the model were allowed to run long enough to resolve particles’ ultimate fate. Agricultural diversions within the Delta increased total entrainment losses and altered local movement patterns. Removable barriers in channels of the southern Delta and gates in the Delta Cross Channel in the northern Delta had minor effects on particles released in the rivers above these channels. A simulation of losses of larval delta smelt showed substantial cumulative losses depending on both inflow and export flow. A simulation mimicking mark–recapture experiments on Chinook salmon smolts suggested that both inflow and export flow may be important factors determining survival of salmon in the upper estuary. To the extent that fish behave passively, this model is probably suitable for describing Delta-wide movement, but it is less suitable for smaller scales or alternative configurations of the Delta.
45 citations
Journal Article•
TL;DR: In this paper, the principal determinants of entrainment losses to the export facilities and how movement of fish through the Delta may be influenced by flow were examined using the Delta Simulation Model-2 hydrodynamic model.
Abstract: Movements of pelagic organisms in the tidal freshwater regions of estuaries are sensitive to the movements of water. In the Sacramento-San Joaquin Delta—the tidal freshwater reach of the San Francisco Estuary—such movements are key to losses of fish and other organisms to entrainment in large water-export facilities. We used the Delta Simulation Model-2 hydrodynamic model and its particle tracking model to examine the principal determinants of entrainment losses to the export facilities and how movement of fish through the Delta may be influenced by flow. We modeled 936 scenarios for 74 different conditions of flow, diversions, tides, and removable barriers to address seven questions regarding hydrodynamics and entrainment risk in the Delta. Tide had relatively small effects on fate and residence time of particles. Release location and hydrology interacted to control particle fate and residence time. The ratio of flow into the export facilities to freshwater flow into the Delta (export:inflow or EI ratio) was a useful predictor of entrainment probability if the model were allowed to run long enough to resolve particles’ ultimate fate. Agricultural diversions within the Delta increased total entrainment losses and altered local movement patterns. Removable barriers in channels of the southern Delta and gates in the Delta Cross Channel in the northern Delta had minor effects on particles released in the rivers above these channels. A simulation of losses of larval delta smelt showed substantial cumulative losses depending on both inflow and export flow. A simulation mimicking mark–recapture experiments on Chinook salmon smolts suggested that both inflow and export flow may be important factors determining survival of salmon in the upper estuary. To the extent that fish behave passively, this model is probably suitable for describing Delta-wide movement, but it is less suitable for smaller scales or alternative configurations of the Delta.
40 citations
TL;DR: In this article, a one-dimensional numerical model was used to investigate the importance of white-capping waves to vertical mixing at a 3-meter-deep site in Franks Tract in the Sacramento-San Joaquin Delta over an 11-day period.
Abstract: A one-dimensional numerical model that simulates the effects of whitecapping waves was used to investigate the importance of whitecapping waves to vertical mixing at a 3-meter-deep site in Franks Tract in the Sacramento-San Joaquin Delta over an 11-day period. Locally-generated waves of mean period approximately 2 s were generated under strong wind conditions; significant wave heights ranged from 0 to 0.3 m. A surface turbulent kinetic energy flux was used to model whitecapping waves during periods when wind speeds > 5 m s-1 (62% of observations). The surface was modeled as a wind stress log-layer for the remaining 38% of the observations. The model results demonstrated that under moderate wind conditions (5–8 m s-1 at 10 m above water level), and hence moderate wave heights, whitecapping waves provided the dominant source of turbulent kinetic energy to only the top 10% of the water column. Under stronger wind (> 8 m s-1), and hence larger wave conditions, whitecapping waves provided the dominant source of turbulent kinetic energy over a larger portion of the water column; however, this region extended to the bottom half of the water column for only 7% of the observation period. The model results indicated that phytoplankton concentrations close to the bed were unlikely to be affected by the whitecapping of waves, and that the formation of concentration boundary layers due to benthic grazing was unlikely to be disrupted by whitecapping waves. Furthermore, vertical mixing of suspended sediment was unlikely to be affected by whitecapping waves under the conditions experienced during the 11-day experiment. Instead, the bed stress provided by tidal currents was the dominant source of turbulent kinetic energy over the bottom half of the water column for the majority of the 11-day period.
39 citations
TL;DR: In this article, the authors summarized almost two decades of historical data and used it to describe their current knowledge of the processes controlling the occurrence of current-use pesticides in the watershed.
Abstract: The occurrence and potential effects of current-use pesticides are of concern in the San Francisco Estuary watershed but our understanding of the spatial and temporal distribution of contamination is limited. This paper summarizes almost two decades of historical data and uses it to describe our current knowledge of the processes controlling the occurrence of current-use pesticides in the watershed. Monitoring studies analyze fewer than half of the pesticides applied in the watershed and most of our knowledge is about inputs of dissolved pesticides in the upper watershed. The four major seasonal patterns of riverine inputs of pesticides to the estuary can be identified by usage and transport mechanism. Dormant spray insecticides applied to orchards and herbicides applied to a variety of crops are transported by rainfall during the winter. Alfalfa pesticides are detected following rainfall and irrigation return flow in the spring, and rice pesticides are detected following release of rice field water in the summer. Irrigation return flows transport a variety of herbicides during the summer. In addition, pesticides applied on Delta islands can cause elevated pesticide concentrations in localized areas. Although not as well characterized, urban creeks appear to have their own patterns of insecticide concentrations causing toxicity throughout most of the year. Current-use pesticides have also been detected on suspended and bed sediments throughout the watershed but limited data make it difficult to determine occurrence patterns. Data gaps include the lack of analysis of many pesticides (or degradates), changing pesticide use, limited information on pesticide transport within the Delta, and an incomplete understanding of the transport and persistence of sediment-associated pesticides. Future monitoring programs should be designed to address these data gaps.
39 citations
TL;DR: In this article, a sample design-based procedure for estimating pre-adult and adult delta smelt abundance is described using data from midwater trawl surveys taken during the months of September, October, November, and December for the years 1990 through 2006 and estimates of size selectivity of the gear from a covered codend experiment.
Abstract: A sample design-based procedure for estimating pre-adult and adult delta smelt abundance is described. Using data from midwater trawl surveys taken during the months of September, October, November, and December for the years 1990 through 2006 and estimates of size selectivity of the gear from a covered codend experiment, stratified random sample ratio estimates of delta smelt abundance were made per month. The estimation procedure is arguably an improvement over the dimensionless delta smelt indices that have been used historically in that (1) the volume sampled is used in a manner that leads to directly interpretable numbers and (2) standard errors are easily calculated. The estimates are quite imprecise, i.e., coefficients of variation in the range of 100\% occurred. The point estimates are highly correlated with the monthly indices, and conclusions on abundance declines are quite similar. However, both the estimates and indices may suffer from selection biases if the trawl samples are not representative of the true densities. Future work is needed in at least three areas: (1) gathering additional information to determine the validity of assumptions made, in particular determining the possible degree of selection bias; (2) developing procedures that utilize survey data gathered from earlier life history stages, such as larval surveys; (3) embedding a life-history model into the population estimation procedure.
33 citations
TL;DR: This analysis focused on peak (maximum) and base (minimum) daily discharge of the annual snowmelt-driven hydrographs from 18 Sierra Nevada watersheds and 24 stream gage locations using standard correlation methods to develop a hydrologic classification of mountain watersheds based on runoff versus base flow as a percentage of peak flow.
Abstract: Sierra Nevada snowpack is a critical water source for California’s growing population and agricultural industry. However, because mountain winters and springs are warming, on average, precipitation as snowfall relative to rain is decreasing, and snowmelt is earlier. The changes are stronger at mid-elevations than at higher elevations. The result is that the water supply provided by snowpack is diminishing. In this paper, we describe principal hydrologic responses to climatic and spatial geologic variations as gleaned from a series of observations including snowpack, stream-flow, and bedrock geology. Our analysis focused on peak (maximum) and base (minimum) daily discharge of the annual snowmelt-driven hydrographs from 18 Sierra Nevada watersheds and 24 stream gage locations using standard correlation methods. Insights into the importance of the relative magnitudes of peak flow and soil water storage led us to develop a hydrologic classification of mountain watersheds based on runoff versus base flow as a percentage of peak flow. Our findings suggest that watersheds with a stronger base flow response store more soil water than watersheds with a stronger peak-flow response. Further, the influence of antecedent wet or dry years is greater in watersheds with high base flow, measured as a percentage of peak flow. The strong correlation between 1) the magnitude of peak flow, and 2) snow water equivalent can be used to predict peak flow weeks in advance. A weaker but similar correlation can be used to predict the magnitude of base flow months in advance. Most of the watersheds show a trend that peak flow is occurring earlier in the year.
20 citations
TL;DR: In this paper, the CALFED Science Program, which serves as an important and illustrative example from among the many current scientific resource and ecosystem management programs, has been recommended as a strategic approach that the scientific and publicpolicy communities in central California, in general, may need to pursue.
Abstract: Current projections of climate change present a number of challenges to scientists and decision-makers. The projections predict a twenty-first-century climate in which many climate variables are likely to trend across broad geographical areas and at rates that are rapid by historical standards. The projections of change are likely to remain uncertain for many years to come, and complete surprises are possible. Responses to these changes will have to span large areas and many variables, and impacts will interact in complex ways. In the face of these challenges, we offer recommendations as to strategic approaches that the CALFED Science Program—which serves here as an important and illustrative example from among the many current scientific resource- and ecosystemmanagement programs—and the scientific and publicpolicy communities in central California, in general, may need to pursue. Recommended strategies include emphasis on long-term eco- and resource-system adaptability—rather than historical verisimilitude—in its restoration targets; major commitments to longterm monitoring of restoration and impacts; even more integration across scientific disciplines, observations, models, and across the study area; increased use of manipulative experiments; and recognition that climate-change issues must be addressed in all efforts undertaken by the program.
16 citations
TL;DR: It is found that all three water quality variables predicted delta smelt occurrence, and three distinct geographic regions that had similar long-term trends in delta Smelt capture probabilities were identified.
Abstract: The biological productivity of river-dominated estuaries is affected strongly by variation in freshwater inflow, which affects nursery habitat quality. Previous research has shown this is generally true in the upper San Francisco Estuary, California, USA; however, one endemic species of high management importance, delta smelt (Hypomesus transpacificus), has shown ambiguous population responses to river inflow variation. We hypothesized that populationlevel associations with abiotic habitat metrics have not been apparent because the effects occur seasonally, and at spatial scales smaller than the entire upper San Francisco Estuary. We tested this hypothesis by applying regression techniques and principal components analysis (PCA) to a long-term data-set (1970–2004) of summertime fish catch, and concurrently measured water quality (specific conductance, Secchi disk depth, and water temperature). We found that all three water quality variables predicted delta smelt occurrence, and we identified three distinct geographic regions that had similar long-term trends in delta smelt capture probabilities. The primary habitat region was centered on the confluence of
TL;DR: In this article, the authors investigated the subsidence reversal potential of two 3 hectare, permanently flooded, impounded wetlands re-established on a deeply subsided field on Twitchell Island.
Abstract: The stability of levees in the Sacramento-San Joaquin Delta is threatened by continued subsidence of Delta peat islands. Up to 6 meters of land-surface elevation has been lost in the 150 years since Delta marshes were leveed and drained, primarily from oxidation of peat soils. Flooding subsided peat islands halts peat oxidation by creating anoxic soils, but net accumulation of new material in restored wetlands is required to recover land-surface elevations. We investigated the subsidence reversal potential of two 3 hectare, permanently flooded, impounded wetlands re-established on a deeply subsided field on Twitchell Island. The shallower wetland (design water depth 25 cm) was almost completely colonized by dense emergent marsh vegetation within two years; whereas, the deeper wetland (design water depth 55 cm) which developed spatially variable depths as a result of heterogeneous colonization by emergent vegetation, still had some areas remaining as open water after nine years. Changes in land-surface elevation were quantified using repeated sedimentation-erosion table measurements. New material accumulating in the wetlands was sampled by coring. Land-surface elevations increased by an average of 4 cm/yr in both wetlands from 1997 to 2006; however, the rates at different sites in the wetlands ranged from -0.5 to +9.2 cm/yr. Open water areas of the deeper wetland without emergent vegetation had the lowest rates of land-surface elevation gain. The greatest rates occurred in areas of the deeper wetland most isolated from the river water inlets, with dense stands of emergent marsh vegetation (tules and cattails). Vegetated areas of the deeper wetland in the transition zones between open water and mature emergent stands had intermediate rates of land-surface gain, as did the entire shallower wetland. These results suggest that the dominant component contributing to land-surface elevation gain in these wetlands was accumulation of organic matter, rather than mineral sediment, and that accumulation of organic matter in emergent marshes is strongly affected by hydrologic factors. Re-established, non-tidal wetlands with managed hydrology can produce significant increases in land-surface elevations, which can help to improve levee stability and protect subsided islands from future flooding.
Journal Article•
TL;DR: The hypothesis that basic water quality parameters are predictors of delta smelt relative abundance, but only at regional spatial scales is supported.
Abstract: The biological productivity of river-dominated estuaries is affected strongly by variation in freshwater inflow, which affects nursery habitat quality Previous research has shown this is generally true in the upper San Francisco Estuary, California, USA; however, one endemic species of high management importance, delta smelt (Hypomesus transpacificus), has shown ambiguous population responses to river inflow variation We hypothesized that population-level associations with abiotic habitat metrics have not been apparent because the effects occur seasonally, and at spatial scales smaller than the entire upper San Francisco Estuary We tested this hypothesis by applying regression techniques and principal components analysis (PCA) to a long-term data-set (1970–2004) of summertime fish catch, and concurrently measured water quality (specific conductance, Secchi disk depth, and water temperature) We found that all three water quality variables predicted delta smelt occurrence, and we identified three distinct geographic regions that had similar long-term trends in delta smelt capture probabilities The primary habitat region was centered on the confluence of the Sacramento and San Joaquin rivers; delta smelt relative abundance was typically highest in the Confluence region throughout the study period There were two marginal habitat regions—including one centered on Suisun Bay—where specific conductance was highest and delta smelt relative abundance varied with specific conductance The second marginal habitat region was centered on the San Joaquin River and southern Sacramento-San Joaquin Delta The San Joaquin region had the warmest water temperatures and the highest water clarity, which increased strongly in this region during 1970–2004 In the San Joaquin region, where delta smelt relative abundance was correlated with water clarity, catches declined rapidly to zero from 1970–1978 and remained consistently near zero thereafter However, when we combined these regional results into estuary-wide means, there were no significant relationships between any of the water quality variables and delta smelt relative abundance Our findings support the hypothesis that basic water quality parameters are predictors of delta smelt relative abundance, but only at regional spatial scales
TL;DR: Sommer et al. as mentioned in this paper examined the potential use of managed inundation to support spawning and rearing of splittail in years when the availability of seasonal habitat is limited.
Abstract: Author(s): Sommer, Ted R.; Harrell, William C.; Matica, Zoltan; Feyrer, Frederick | Abstract: Although there is substantial information about the benefits of managed seasonal wetlands to wildlife, little is known about whether this habitat can help support “at risk” native fishes. The Sacramento splittail Pogonichthys macrolepidotus, a California Species of Special Concern, does not produce strong year classes unless it has access to floodplain wetlands of the San Francisco Estuary and its tributaries. Our study examined the potential use of managed inundation to support spawning and rearing of splittail in years when the availability of seasonal habitat is limited. Wild adult splittail were captured during their spawning migration and transferred to a 3.8-ha engineered wetland, where they successfully spawned shortly after introduction. Radio telemetry studies suggested that post-spawning adults were relatively sedentary over the study period. Adult splittail were primarily located in habitats with open water or light vegetation, and in the deepest portions of the wetland. Snorkel surveys showed that early stages (mean 21-mm fork length [FL]) of young splittail produced in the wetland were strongly associated with shallow areas with shoreline emergent terrestrial vegetation and submerged aquatic vegetation, but moved offshore to deeper areas with tules and submerged terrestrial vegetation at night. Larger juveniles (mean 41-mm FL) primarily used deeper, offshore habitats during day and night. At night, schools of both younger and older juveniles dispersed, and individuals were associated with the bottom of the water column. These observations have important implications for the construction of managed and restored wetlands for the benefit of native fishes.