San Francisco Estuary and Watershed Science

To evaluate the role of restoration in the recovery of the Delta ecosystem, we need to have clear targets and performance measures that directly assess ecosystem function. Primary production is a crucial ecosystem process, which directly limits the quality and quantity of food available for secondary consumers such as invertebrates and fish. The Delta has a low rate of primary production, but it is unclear whether this was always the case. Recent analyses from the Historical Ecology Team and Delta Landscapes Project provide quantitative comparisons of the areal extent of 14 habitat types in the modern Delta versus the historical Delta (pre-1850). Here we describe an approach for using these metrics of land use change to: (1) produce the first quantitative estimates of how Delta primary production and the relative contributions from five different producer groups have been altered by large-scale drainage and conversion to agriculture; (2) convert these production estimates into a common currency so the contributions of each producer group reflect their food quality and efficiency of transfer to consumers; and (3) use simple models to discover how tidal exchange between marshes and open water influences primary production and its consumption. Application of this approach could inform Delta management in two ways. First, it would provide a quantitative estimate of how large-scale conversion to agriculture has altered the Delta's capacity to produce food for native biota. Second, it would provide restoration practitioners with a new approach—based on ecosystem function—to evaluate the success of restoration projects and gauge the trajectory of ecological recovery in the Delta region.

This paper reviews and highlights recent research findings on food web processes since an earlier review by Kimmerer et al. (2008). We conduct this review within a conceptual framework of the Delta–Suisun food web, which includes both temporal and spatial components. The temporal component of our framework is based on knowledge that the landscape has changed markedly from historical conditions. The spatial component of our framework acknowledges that the food web is not spatially static; it varies regionally and across habitat types within regions. The review highlights the idea of a changing baseline with respect to food web function. New research also indicates that interactions between habitat-specific food webs vary across the current landscape. For example, based on early work in the south Delta, the food web associated with submerged aquatic vegetation was thought to provide little support to species of concern; however, data from other regions of the estuary suggest that this conceptual model may not apply across the entire region. Habitat restoration has been proposed as a method of re-establishing historic food web processes to support species of concern. Benefits are likely for species that directly access such restored habitats, but are less clear for pelagic species. Several topics require attention to further improve the knowledge of food webs needed to support effective management, including: (1) synthesis of factors responsible for low pelagic biomass; (2) monitoring and research on effects of harmful algal blooms; (3) broadening the scope of long-term monitoring; (4) determining benefits of tidal wetland restoration to species of concern, including evaluations of interactions of habitat-specific food webs; and (5) interdisciplinary analysis and synthesis. The only certainty is that food webs will continue to change in response to the changes in the physical environment and new species invasions.

Anthropogenic climate change amounts to a rapidly approaching, “new” stressor in the Sacramento–San Joaquin Delta system. In response to California’s extreme natural hydroclimatic variability, complex water-management systems have been developed, even as the Delta’s natural ecosystems have been largely devastated. Climate change is projected to challenge these management and ecological systems in different ways that are characterized by different levels of uncertainty. For example, there is high certainty that climate will warm by about 2°C more (than late-20th-century averages) by mid-century and about 4°C by end of century, if greenhouse-gas emissions continue their current rates of acceleration. Future precipitation changes are much less certain, with as many climate models projecting wetter conditions as drier. However, the same projections agree that precipitation will be more intense when storms do arrive, even as more dry days will separate storms. Warmer temperatures will likely enhance evaporative demands and raise water temperatures. Consequently, climate change is projected to yield both more extreme flood risks and greater drought risks. Sea level rise (SLR) during the 20th century was about 22 cm, and is projected to increase by at least 3-fold this century. SLR together with land subsidence threatens the Delta with greater vulnerabilities to inundation and salinity intrusion. Effects on the Delta ecosystem that are traceable to warming include SLR, reduced snowpack, earlier snowmelt and larger storm-driven streamflows, warmer and longer summers, warmer summer water temperatures, and water-quality changes. These changes and their uncertainties will challenge the operations of water projects and uses throughout the Delta’s watershed and delivery areas. Although the effects of of climate change on Delta ecosystems may be profound, the end results are difficult to predict, except that native species will fare worse than invaders. Successful preparation for the coming changes will require greater integration of monitoring, modeling, and decision making across time, variables, and space than has been historically normal.

Much of the water supplied in California for agriculture and cities is taken directly from the Sacramento–San Joaquin Delta (Delta) or indirectly from surface and groundwater diversions upstream. These water supplies have great economic and social value, and considerable ecosystem effects. Long thought of as the major source of water for economic growth in California, the reliability of water supplied from the Delta is threatened by drought, flood, climate change, earthquakes, growing water demands, and deteriorating conditions for endangered species and native ecosystems. Research in recent years has improved understanding of how management of the Delta ties together the quantity and quality of water available statewide. These ties run from the Sierra mountains and coastal streams, through the Central Valley, to the San Francisco Bay Area, and over the Tehachapi Mountains to southern California. For decades, Californians counted on reducing Delta outflows to supply water for growing water demands in its watershed and in water importing areas. With greater competition for water, concern for environmental effects, and a changing climate, the reliability of such supplies is now diminishing. This must lead to tighter accounting and modeling of water supplies in the Delta and throughout its watershed. This paper reviews issues about Delta water supplies, operations, regulations, and reliability; the economic value of supply; costs of unreliability in quantity and quality; and several directions for further scientific and technical work on water supply reliability.

We studied zooplankton distributions in the upper San Francisco Estuary at nested scales of tens to thousands of meters. The purposes of the study were to assess how well the Interagency Ecological Program (IEP) zooplankton monitoring represents abundance, and to investigate the variability of plankton on scales similar to those of foraging by fish. Samples were taken at three sites in the western Sacramento–San Joaquin Delta. We took 18 sets of six samples each with a plankton net along transects from near shore to center channel, and six sets of ten samples in the vicinity of a drifter either in mid-channel or near shore. Sampling took place in June–July 2014 during neap and spring tides, ebb and flood, day and night (transects only). Analysis focused on three common copepod species. Transect samples showed little consistent variation along transects, except that Pseudodiaptomus forbesi was less abundant nearshore than offshore by day at Big Break, the most landward site. The ratio of adults to adults + copepodites was strongly and positively related to turbidity by day but not by night, indicating demersal behavior. Drifter samples showed a minimum standard deviation of log10 sample counts of about 0.1, indicating that about two-thirds of replicate abundance values were within 80 % to 125% of the mean. A measure of difference between plankton samples at pairs of sample points was unrelated to distance between sample points for drifter samples, weakly related along transects for Limnoithona spp. stages, and strongly related for P. forbesi mainly because of the along-transect gradients at Big Break. The IEP sampling program is representative of plankton abundance except for demersal organisms, which can be ten-fold more abundant by night than by day. Small planktivorous fish could forage in patches of up to ~25% higher abundance than the mean.

Outflow from the Sacramento–San Joaquin Delta is a key parameter used in the management of the San Francisco Bay–Delta system. At present we can estimate this by assuming a steady state balance of inflows and outflows (Dayflow) or by direct measurement. In this paper, I explore differences between observed sub-tidal variations in measured outflow and Dayflow values using water level and flow data taken during the summer of 2015 and an analytical framework based on the sub-tidally filtered St. Vénant equations. This analysis shows that flows associated with sub-tidal water level variations in the Delta explain most of the difference between the two flow measures. These variations largely result from low-frequency variations in sea level in the coastal ocean and to wind stresses acting on Suisun Bay, with spring–neap variations in tides playing a lesser role. Overall, a comparison of Dayflow and the direct flow measurement for water years 2008 to 2014 shows that the two flow measures are in good agreement, although the root mean square difference between the two values (ca. 5,000 cfs) is comparable to—or larger than—typical low flow values of Dayflow.