SFEWS: Volume 19, Issue 2
Welcome to the June issue of San Francisco Estuary and Watershed Science. At midyear in 2021, research surrounding the San Francisco Estuary looks forward. Here, six articles in four categories offer advances in science using new technologies and a re-examination of past efforts.
Photo: CA Dept. of Water Resources, public domain.
In Honor of Dr. Larry R. Brown
Herbold et al. remember Dr. Larry R. Brown, who died suddenly in February of 2021. This note captures how important his scientific work was in the San Francisco Estuary and why he will be intensely missed by many of his colleagues.
Photo: Canva stock image
Preparing Scientists, Policymakers, and Managers for a Fast-Forward Future
To accelerate forward-looking science, policy, and management in the Delta, Norgaard et al. propose that the State of California create a Delta Science Visioning Process to fully and openly assess the challenges of more rapid change to science, policy, and management and offer appropriate solutions, including legislation.
Photo: CA Dept. of Water Resources, public domain
Ecological Effects of Climate-Driven Salinity Variation in the San Francisco Estuary: Can We Anticipate and Manage the Coming Changes?
Ghalambor et al. review and summarize the presentations and discussions that arose during the symposium “Ecological and Physiological Impacts of Salinization of Aquatic Systems from Human Activities,” which brought together an interdisciplinary group of scientists, managers, and policy-makers to answer the central question: can we use existing knowledge and future projections to predict and manage anticipated ecological impacts?
Photo: Canva stock image
Effects of Tidally Varying River Flow on Entrainment of Juvenile Salmon into Sutter and Steamboat Slough
Previous studies suggest that fish generally “go with the flow”—however, complex tidal hydrodynamics at sub-daily time-scales may be decoupled from net flow. To further examine entrainment of acoustically tagged juvenile Chinook Salmon into Sutter and Steamboat sloughs, Romine et al. modeled routing of acoustic tagged juvenile salmon as a function of tidally varying hydrodynamic data. Results indicate that discharge, the proportion of flow that entered the slough, and the rate of change of flow were good predictors of the probability of an individual fish being entrained.
Photo: John Burau
Examining Retention-at-Length of Pelagic Fishes Caught in the Fall Midwater Trawl Survey
A study was conducted in 2014-2015 to investigate and quantify the efficiency of the Fall Midwater Trawl for catching the endangered fish species Delta Smelt (Hypomesus transpacificus). Mitchell and Baxter revisit the same gear efficiency study and further utilize the data set by fitting selectivity curves for three additional pelagic fish species: Threadfin Shad (Dorosoma petenense), American Shad (Alosa sapidissima), and Mississippi Silverside (Menidia beryllina), and by applying more statistically sensitive approaches.
Photo: Lara Mitchell
Use of the SmeltCam as an Efficient Fish Sampling Alternative Within the San Francisco Estuary
Resource managers often rely on long-term monitoring surveys to detect trends in biological data. However, no survey gear is 100% efficient, and many sources of bias can both detect or miss biological trends. Huntsman et al. evaulate the SmeltCam, an imaging apparatus developed as a sampling alternative to long-term trawling gear surveys within the San Francisco Estuary, with the potential to reduce handling stress on sensitive species like the Delta Smelt (Hypomesus transpacificus).
Photo: Ken Newman
Volume 6, Issue 1, 2008
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.
Phytoplankton in the Upper San Francisco Estuary: Recent Biomass Trends, Their Causes, and Their Trophic Significance
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.
Principal Hydrologic Responses to Climatic and Geologic Variability in the Sierra Nevada, California
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.
Investigating Particle Transport and Fate in the Sacramento–San Joaquin Delta Using a Particle-Tracking Model
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.