San Francisco Estuary and Watershed Science

The State of Bay–Delta Science 2016 (SBDS) is a collection of papers that summarizes the scientific understanding of the Sacramento–San Joaquin Delta, emphasizing progress made during the past decade.It builds on the first SBDS edition (Healey et al. 2008). Paper topics for this edition address the most relevant scientific issues in the Delta identified by senior scientists and managers. The topical papers cover issues ranging from contaminants in the Delta to levee stability, and from Delta food webs to recent discoveries about salmon migration. These papers are written for a scientific audience. Two additional papers, one describing the challenges of managing water and ecosystems in the Delta and another that discusses policy implications of the recent scientific findings, are written for a general audience. The papers will be published in at least two issues of San Francisco Estuary and Watershed Science and will be available as a set electronically.

The State of Bay-Delta Science, 2008 (Healey et al. 2008). The Delta Smelt is endemic to the upper San Francisco Estuary. Much of its historic habitat is no longer available and remaining habitat is increasingly unable to sustain the population. As a listed species living in the central node of California’s water supply system, Delta Smelt has been the focus of a large research effort to understand causes of decline and identify ways to recover the species. Since 2008, a remarkable record of innovative research on Delta Smelt has been achieved, which is summarized here. Unfortunately, research has not prevented the smelt’s continued decline, which is the result of multiple, interacting factors. A major driver of decline is change to the Delta ecosystem from water exports, resulting in reduced outflows and high levels of entrainment in the large pumps of the South Delta. Invasions of alien species, encouraged by environmental change, have also played a contributing role in the decline. Severe drought effects have pushed Delta Smelt to record low levels in 2014–2015. The rapid decline of the species and failure of recovery efforts demonstrate an inability to manage the Delta for the “co-equal goals” of maintaining a healthy ecosystem and providing a reliable water supply for Californians. Diverse and substantial management actions are needed to preserve Delta Smelt.

As juvenile salmon enter the Sacramento–SanJoaquin River Delta (“the Delta”) they disperse among its complex channel network where they are subject to channel-specific processes that affect their rate of migration, vulnerability to predation, feeding success, growth rates, and ultimately, survival. In the decades before 2006, tools available to quantify growth, dispersal, and survival of juvenile salmon in this complex channel network were limited.Fortunately, thanks to technological advances such as acoustic telemetry and chemical and structural otolith analysis, much has been learned over the past decade about the role of the Delta in the life cycle of juvenile salmon. Here, we review new science between 2006and 2016 that sheds light on how different life stages and runs of juvenile salmon grow, move, and survive in the complex channel network of the Delta. One of the most important advances during the past decade has been the widespread adoption of acoustic telemetry techniques. Use of telemetry has shed light on how survival varies among alternative migration routes and the proportion of fish that use each migration route. Chemical and structural analysis of otoliths has provided insights about when juveniles left their natal river and provided evidence of extended rearing in the brackish or saltwater regions of the Delta. New advancements in genetics now allow individuals captured by trawls to be assigned to specific runs. Detailed information about movement and survival in the Delta has spurred development of agent-based models of juvenile salmon that are coupled to hydrodynamic models. Although much has been learned, knowledge gaps remain about how very small juvenile salmon (fry and parr) use theDelta. Understanding how all life stages of juvenile salmon grow, rear, and survive in the Delta is critical for devising management strategies that support a diversity of life history strategies.

The Sacramento–San Joaquin Delta (Delta) is a heterogeneous, highly modified aquatic system. I reviewed relevant predator–prey theory, and described extant data on predator–prey relationships of Delta fishes. I ranked predator consumption rates as occasional, moderate, and common, based on frequency-of-occurrence data, and evaluated the frequency, and hypothesized the effects of predation on native and invasive species. I identified 32 different predator categories and 41 different prey categories. Most predators were occasional consumers of individual prey species, although I also observed moderate and common consumption of some prey types. My analysis yielded few generalizations regarding predator–prey interactions for Delta fishes; most predators consumed a variety of both native and invasive fishes. The only evidence for predator specialization on either native or invasive fishes occurred in Prickly Sculpin which, when it consumed fishes, ate mostly native species. Both Striped and Largemouth Bass exhibited wide dietary breadth, preying upon 32 and 28 categories of fish prey respectively. Sacramento Pikeminnow, a native predator, also displayed wide dietary breadth of piscine prey, with 14 different prey categories consumed. Data for reptilian, avian, and mammalian predators were sparse; however, these predators may be significant fish predators in altered habitats or when hatchery salmonids are released. The database for predators and their fish prey was not strong, and I recommend long-term dietary studies combined with prey availability and behavioral and experimental studies to establish predator preferences and anti-predator behaviors, rather than just consumption. The behavioral effects of contaminants on prey species also warrant further examination. Although it has been suggested that a reduction in the Striped Bass population be implemented to reduce predation mortality of Chinook Salmon, the large number of salmon predators in the Delta make it unlikely that this effort will significantly affect salmon mortality.

What happens at one place in a landscape influences and is influenced by what happens in other places. Consequently, management and restoration that focus on individual places may fail to recognize and incorporate interactions across entire landscapes. The science of landscape ecology, which emphasizes the interplay of landscape structure, function, and change at multiple scales, offers a perspective that can integrate the spatial relationships of ecological processes and the functional interconnections of land and water in the Delta. Although the Delta is one of the most studied estuaries in the world, applications of landscape science have been limited. We describe why it is important to incorporate landscape science into management and restoration, emphasizing how Delta landscapes have changed over the past centuries. The land–water linkages of the past have been broken, waterways have been over-connected, and hard boundaries have replaced the gradual and dynamic transitions among landscape patches. The contemporary landscape also has new, novel assemblages of species and stressors that were not there in the past. This historical perspective indicates how knowledge of past landscape functions can contribute to the restoration and management of contemporary landscapes. We illustrate these points with case studies of inundation dynamics and riparian woodlands, and use a third example to describe a landscape approach to restoration. We propose that science that encompasses the multiple, interacting components of functional landscapes in the Delta will foster resilient and enduring restoration and management outcomes that benefit both people and wildlife. We suggest several ways of moving landscape science to the forefront of management and restoration in the Delta.

Groundwater management is important and challenging, and nowhere is this more evident than in California. Managed aquifer recharge (MAR) projects can play an important role in ensuring California manages its groundwater sustainably. Although the benefits and economic costs of surface water storage have been researched extensively, the benefits and economic costs of MAR have been little researched. Historical groundwater data are sparse or proprietary within the state, often impairing groundwater analyses. General obligation bonds from ballot propositions offer a strategic means of mining information about MAR projects, because the information is available publicly. We used bond-funding applications to identify anticipated MAR project benefits and proposed economic costs. We then compared these costs with actual project costs collected from a survey, and identified factors that promote or limit MAR. Our analysis indicates that the median proposed economic cost for MAR projects in California is $410 per acre-foot per year ($0.33 per cubic meter per year). Increasing Water Supply, Conjunctive Use, and Flood Protection are the most common benefits reported. Additionally, the survey indicates that (1) there are many reported reasons for differences between proposed and actual costs ($US 2015) and (2) there is one primary reason for differences between proposed recharge volumes and actual recharge volumes (AFY): availability of source water for recharge. Although there are differences between proposed and actual costs per recharge volume ($US 2015/AFY), the ranges for proposed costs per recharge volume and actual costs per recharge volume for the projects surveyed generally agree. The two most important contributions to the success of a MAR project are financial support and good communication with stakeholders.

California precipitation varies more dramatically from year to year than elsewhere in the conterminous United States. This paper analyzes the extent to which contributions of the wettest days to overall precipitation dictate the state’s precipitation seasonality and frequent multiyear periods of drought (as precipitation deficit) and plenty is analyzed, historically and in projections of future climates. The wettest 5% of wet days in California contribute about a third of precipitation but about two-thirds of the variance of water-year precipitation. Year-to-year fluctuations in precipitation strongly reflect year-to-year fluctuations of contributions from the largest storms, with the large-storm contributions explaining about twice as much precipitation fluctuation as do contributions from all remaining storms combined. This extreme dominance of large storms is largely unique to California within the United States. In climate-change projections, eight of ten climate models considered here yield increases in precipitation from the largest storms, and when the increases are large, total precipitation follows suit. All of the models project declines in contributions from the smaller storms and models projecting total-precipitation declines reflect this decline. Projected changes in variance of water-year precipitation reflect changes in variance of large-storm contributions. The disproportionately large overall contributions from California’s largest storms, and their outsized year-to-year variability, ensure that the state’s largest storms dictate the state’s regimes of wet and dry spells, historically and in climate-change projections.

We applied a water balance model to predict tidally averaged (subtidal) flows through the Old River and Middle River corridor in the Sacramento–San Joaquin Delta. We reviewed the dynamics that govern subtidal flows and water levels and adopted a simplified representation. In this water balance approach, we estimated ungaged flows as linear functions of known (or specified) flows. We assumed that subtidal storage within the control volume varies because of fortnightly variation in subtidal water level, Delta inflow, and barometric pressure. The water balance model effectively predicts subtidal flows and approaches the accuracy of a 1–D Delta hydrodynamic model. We explore the potential to improve the approach by representing more complex dynamics and identify possible future improvements.

The UnTRIM hydrodynamic model was applied to San Francisco Bay and the Sacramento–San Joaquin Delta (Delta) using a coarse-resolution model grid with bathymetry represented at a finer subgrid scale. We simulated a 35-year period, spanning from January 1, 1980 through December 31, 2014. This simulation was used to develop salinity distribution maps to facilitate visualization of fish distribution and abundance data. We compared predicted salinity from the coarse-grid UnTRIM Bay–Delta model to continuous salinity monitoring observations as well to the measured surface salinity from San Pablo Bay through the Delta at a total of 5,542 times and locations where surface salinity was observed as part of several long-term fish monitoring programs: the Fall Midwater Trawl, Summer Townet Survey, and San Francisco Bay Study. The coarse-grid UnTRIM Bay–Delta model was shown to accurately predict hydrodynamics and the spatial distribution of salinity over both a 3-year detailed validation period and over the full 35-year analysis period. The predicted salinity was used to calculate the daily position of X2 and the daily-averaged area of the Low Salinity Zone (LSZ) for each day during the 35-year simulation. Our analysis highlights the influence of multi-year climate patterns, shorter-duration weather patterns, and Delta outflow on salinity distribution. We used the predicted salinity to develop maps of salinity distribution over seven periods for six fish species, and combined the salinity maps with historic fish sampling data to allow for visualization of fish abundance and distribution for 33 years between 1980 and 2012. These maps can be used to explore how different species respond to annual differences in salinity distributions in the San Francisco Estuary, and to expand the understanding of the relationships among salinity and fish abundance, distribution, and population resiliency.