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 14, Issue 1, 2016
Abundance Trends, Distribution, and Habitat Associations of the Invasive Mississippi Silverside (Menidia audens) in the Sacramento–San Joaquin Delta, California, USA
Although many alien fish species have colonized the Sacramento–San Joaquin Delta (Delta), few are as pervasive and abundant as Mississippi Silversides (Menidia audens). Moreover, Mississippi Silversides are hypothesized to be an intra-guild predator of the endangered Delta Smelt (Hypomesus transpacificus). Because of their prevalence in the Delta and poten-tial predation on Delta Smelt, Mississippi Silversides may have far-reaching effects on both the aquatic ecosystem and conservation management policies of the region. Yet little is known about how Mississippi Silverside abundance and distribution have changed within the Delta, or how they respond to various habitat attributes such as temperature, turbidity, and flow. We examined 19 years of beach seine survey data to evaluate how the abundance and distribution of Mississippi Silversides has changed over the years, characterize their habitat associations, and determine the environmental factors that predict their annual cohort strength. Concurrent with the decline of sev-eral pelagic fish species in the San Francisco Estuary in the early 2000s, we observed a significant increase in Mississippi Silverside catch that was accompanied by a moderate distributional shift in which densi-ties increased in the western Delta region. We also found that the occurrence of this highly prolific alien species was associated with higher water tempera-ture, higher turbidity, relatively low conductivity, and moderate to high levels of dissolved oxygen. Lastly, we demonstrated that freshwater input to the Sacramento–San Joaquin Delta during the summer and water exports during the spring months were both negatively correlated with the annual cohort size of Mississippi Silversides in the region. Our study identified the environmental variables deserv-ing additional attention in future studies involving Mississippi Silverside and suggests that the species favors habitat conditions that are likely to be detri-mental for pelagic species such as Delta Smelt.
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Linking Hydrodynamic Complexity to Delta Smelt (Hypomesus transpacificus) Distribution in the San Francisco Estuary, USA
Long-term fish sampling data from the San Francisco Estuary were combined with detailed three-dimensional hydrodynamic modeling to investigate the relationship between historical fish catch and hydrodynamic complexity. Delta Smelt catch data at 45 stations from the Fall Midwater Trawl (FMWT) survey in the vicinity of Suisun Bay were used to develop a quantitative catch-based station index. This index was used to rank stations based on historical Delta Smelt catch. The correlations between historical Delta Smelt catch and 35 quantitative metrics of environmental complexity were evaluated at each station. Eight metrics of environmental conditions were derived from FMWT data and 27 metrics were derived from model predictions at each FMWT station. To relate the station index to conceptual models of Delta Smelt habitat, the metrics were used to predict the station ranking based on the quantified environmental conditions. Salinity, current speed, and turbidity metrics were used to predict the relative ranking of each station for Delta Smelt catch. Including a measure of the current speed at each station improved predictions of the historical ranking for Delta Smelt catch relative to similar predictions made using only salinity and turbidity. Current speed was also found to be a better predictor of historical Delta Smelt catch than water depth. The quantitative approach developed using the FMWT data was validated using the Delta Smelt catch data from the San Francisco Bay Study. Complexity metrics in Suisun Bay were evaluated during 2010 and 2011. This analysis indicated that a key to historical Delta Smelt catch is the overlap of low salinity, low maximum velocity, and low Secchi depth regions. This overlap occurred in Suisun Bay during 2011, and may have contributed to higher Delta Smelt abundance in 2011 than in 2010 when the favorable ranges of the metrics did not overlap in Suisun Bay.
Physical Controls on the Distribution of the Submersed Aquatic Weed Egeria densa in the Sacramento–San Joaquin Delta and Implications for Habitat Restoration
The invasive aquatic plant Egeria densa (Brazilian waterweed) is a submersed aquatic plant that has expanded its distribution in both its native and introduced range. Because the plant grows so densely, it can become a problem for management of waterways and habitat restoration projects. It is difficult to remove once established and mechanical and chemical controls have shown limited effectiveness. Here we analyze the distribution of E. densa in the Sacramento–San Joaquin Delta (the Delta) of California, USA, using environmental variables that include mean water velocity, mean water turbidity, and water column depth. We found that increasing water column depth strongly limited E. densa occurrence, especially when depth at mean lower low water (MLLW) exceeds 2 m. The highest probability of occurrence occurred at locations with a water column depth of −1 to 2 m at MLLW. Turbidity had a reliably negative effect on E. densa occurrence; as water clarity has increased in the Delta, it has likely favored the spread of the plant. Neither mean water velocity nor maximum water velocity had a reliable effect on E. densa probability, in spite of scientific and observational evidence that it is sensitive to flows. These results suggest potentially serious problems with restoration projects that emphasize shallow water habitat in the range favored by E. densa. Without some way to manage spread of the plant—through spraying, sediment loading, or gating—channels in such projects are at risk of being taken over by E. densa. However, these results should be interpreted in light of the fact that water outflow in water year 2008 was very low, and that E. densa abundance may be partially controlled by higher water flows than those considered here.
Multi-Purpose Optimization for Reconciliation Ecology on an Engineered Floodplain: Yolo Bypass, California
Floodplains in California and elsewhere are productive natural habitats with high levels of biodiversity, yet today they are often permanently disconnected from rivers by urban or agricultural development and flood management structures. This disconnection poses a threat to many native fish, bird and other species that evolved to take advantage of seasonal floodplain inundation. The traditional restoration approach to this problem is to recreate historical floodplain by restoring natural hydrologic and successional processes. However levees, dams, and development have made this largely impossible in much of the developed world. Reconciliation ecology recognizes this limitation, and encourages instead the re-engineering of human dominated landscapes to allow for coexistence of native species and human uses. Flood control bypasses are particularly promising places to reconcile historical fish and bird uses of floodplain habitats with human uses. However, the reconciliation approach requires nuanced management of a complex system. Using the Yolo Basin flood bypass in California’s Central Valley as an example, this study develops formal multi-objective optimization to help planners identify management options that best improve habitat quality for fish and birds with minimal costs to farmers or wetland managers. Models like the one developed here can integrate large amounts of data and knowledge, and offer an explicit accounting of relationships and trade-offs between different objectives. This is especially useful in reconciliation planning, where many uses and variables interact on a landscape, and deliberate re-engineering requires consideration of many decisions simultaneously. Initial results suggest that modest land-use changes and inundation management strategies can significantly improve seasonal bird and fish habitat quality at little cost to farmers or other human land uses. The model applications demonstrate the usefulness of multi-objective optimization in reconciling managed floodplains, and provide a framework for integrating new knowledge and testing varying assumptions to improve management over time.
Reservoir operating rules for water resource systems are typically developed by combining intuition, professional discussion, and simulation modeling. This paper describes a joint optimization–simulation approach to develop preliminary economically-based operating rules for major reservoirs in California’s Sacramento Valley, based on optimized results from CALVIN, a hydro-economic optimization model. We infer strategic operating rules from the optimization model results, including storage allocation rules to balance storage among multiple reservoirs, and reservoir release rules to determine monthly release for individual reservoirs. Results show the potential utility of considering previous year type on water availability and various system and sub-system storage conditions, in addition to normal consideration of local reservoir storage, season, and current inflows. We create a simple simulation to further refine and test the derived operating rules. Optimization model results show particular insights for balancing the allocation of water storage among Shasta, Trinity, and Oroville reservoirs over drawdown and refill seasons, as well as some insights for release rules at major reservoirs in the Sacramento Valley. We also discuss the applicability and limitations of developing reservoir operation rules from optimization model results.
Surface water and groundwater management are often tightly linked, even when linkage is not intended or expected. This link is especially common in semi-arid regions, such as California. This paper summarizes a modeling study on the effects of ending long-term overdraft in California’s Central Valley, the state’s largest aquifer system. The study focuses on economic and operational aspects, such as surface water pumping and diversions, groundwater recharge, water scarcity, and the associated operating and water scarcity costs. This analysis uses CALVIN, a hydro-economic optimization model for California’s water resource system that suggests operational changes to minimize net system costs for a given set of conditions, such as ending long-term overdraft. Based on model results, ending overdraft might induce some major statewide operational changes, including large increases to Delta exports, more intensive conjunctive-use operations with increasing artificial and in-lieu recharge, and greater water scarcity for Central Valley agriculture. The statewide costs of ending roughly 1.2 maf yr-1 of groundwater overdraft are at least $50 million per year from additional direct water shortage and additional operating costs. At its worst, the costs of ending Central Valley overdraft could be much higher, perhaps comparable to the recent economic effects of drought. Driven by recent state legislation to improve groundwater sustainability, ending groundwater overdraft has important implications statewide for water use and management, particularly in the Sacramento–San Joaquin Delta. Ending Central Valley overdraft will amplify economic pressure to increase Delta water exports rather than reduce them, tying together two of California’s largest water management problems.