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State of Bay-Delta Science 2016


The State of Bay–Delta Science (SBDS) 2016 is a collection of papers that represents a synthesis of the current scientific understanding of the Delta, emphasizing progress made on key research questions during the past decade and identifying remaining knowledge gaps.


SBDS 2016 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 and were published in the July, October, and December 2016 issues of the online journal San Francisco Estuary and Watershed Science. 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.


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The State of Bay-Delta Science 2016: An Introduction

The first edition of SBDS presented seven shifts in perspective or changes in the way that scientists understood the Delta and water supply that had emerged in the decade before its publication (Healey et al. 2008). These changes in scientific understanding have profoundly affected the long-term vision for the Delta and the way that it is managed (Delta Vision Task Force 2008; Delta Stewardship Council 2010).


A similar evolution in understanding has emerged in the eight years since publication of the first edition of SBDS, and we expect our understanding of the Delta and California water will continue to evolve and change as new studies are conducted. SBDS will be a living document, updated from time to time as sufficient new findings accumulate and, in particular, as the effects of climate change become more apparent.


Meeting the new and unprecedented challenges to water supply and ecosystem conservation that climate change will bring will require both an intensification of scientific effort and much better coordination and planning of Delta science. The papers that make up the second edition of SBDS represent one step toward an integrated and policy-relevant compilation of science in the Delta.


Read the full introduction here



Delta Smelt: Life History and Decline of a Once-Abundant Species

in the San Francisco Estuary

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 and diverse and substantial management actions are needed to preserve delta smelt.


Read the full chapter here



Anadromous Salmonids in the Delta: New Science 2006-2016

As juvenile salmon enter 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 channel network were limited. Fortunately, thanks to technological advances, much has been learned over the past decade about the role of the Delta in the life cycle of juvenile salmon.


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 have 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 the Delta. 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.


 Read the full chapter here



Predation on Fishes in the Sacramento–San Joaquin Delta: Current Knowledge and Future Directions

The Delta is a diverse, highly modified aquatic system. This paper reviews relevant predator–prey theory, describes data on predator–prey relationships of Delta fishes, ranks predator consumption rates, and presents hypotheses for the effects of predation on native and invasive species. Thiry-two different predator categories and 41 different prey categories are identified.


The analysis yielded few generalizations regarding predator–prey interactions for Delta fishes. The only evidence for predator specialization occurred in Prickly Sculpin which, when it consumed fishes, ate mostly native species. 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 long-term dietary studies combined with prey availability and behavioral and experimental studies are needed. 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.


Read the full chapter here



The Delta as Changing Landscapes

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 inds, offers a perspective that can combine the spatial relationships anividual 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 scaled 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. The authors 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. The authors illustrate these points with case studies of inundation dynamics and riparian woodlands, and use a third example to describe a landscape approach to restoration. The authors 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. The authors suggest several ways of moving landscape science to the forefront of management and restoration in the Delta.


Read the full chapter here



Food Webs of the Delta, Suisun Bay, and Suisun Marsh:

An Update on Current Understanding and Possibilities for Management

This paper reviews recent research findings on food web processes since 2008. It also highlights the idea of a changing baseline with respect to food web function. New research 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 underwater 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 issues 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.


Read the full chapter here



Climate Change and the Delta

Climate change amounts to a fast 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. Future precipitation changes are less certain, with as many climate models projecting wetter conditions as drier. Warmer temperatures will likely enhance evaporation and raise water temperatures. Consequently, climate change is projected to yield both more extreme flood risks and greater drought risks.


Effects on the Delta ecosystem that are traceable to warming include sea level rise, reduced snowpack, earlier snowmelt and larger storm-driven streamflow, 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 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.


Read the full chapter here



California’s Agricultural and Urban Water Supply Reliability

and the Sacramento–San Joaquin Delta

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.


Much of the water supplied in California for agriculture and urban use is taken directly from the Sacramento–San Joaquin Delta or indirectly from surface and groundwater diversions upstream. These water supplies have great economic and social value, and considerable effects on the ecosystem. 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 our understanding of how management of the Delta ties together the quantity and quality of water available statewide. For decades, Californians counted on reducing Delta outflows to supply water for increasing 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.


Read the full chapter here


Recent advances in understanding flow dynamics and transport of water-quality constituents in the Sacramento–San Joaquin River Delta

This chapter describes advances during the past decade in understanding flow dynamics and how water-quality constituents, such as salinity, heat, oxygen, nutrients, contaminants, and more, move within California’s Sacramento-San Joaquin River Delta. Water-quality constituents are affected by water diversions and other human manipulations of flow and they greatly affect the quantity and quality of habitats in the Delta.


Along with human intervention, the Pacific Ocean, the Central Valley watershed, and the atmosphere, are a few drivers of flow and transport in the Delta. These drivers provide a conceptual framework for presenting recent findings. The tremendous expansion of acoustic and optical instruments utilized in the Delta over the past decade has greatly improved our understanding of how tidal variability affects flow and transport. Sediment is increasingly viewed as a diminishing resource needed to sustain habitat and tidal marsh, especially as sea level rises.


Connections between the watershed, Delta, and San Francisco Bay that have been studied recently highlight that a landscape view of this system is needed rather than consideration of each region individually. Interactions of multiple drivers and information gaps are discussed.


Read the full chapter here



An overview of multi-dimensional models of the Sacramento-San Joaquin Delta

Over the past fifteen years, the development and application of models in San Francisco Bay and the Sacramento-San Joaquin Delta has transformed our ability to analyze and understand the underlying physics of the system.


Initial applications of three-dimensional models focused primarily on salt intrusion, and provided a valuable resource for investigating how sea level rise and levee failures in the Delta could influence water quality in the Delta in the future. However, multi-dimensional models have also provided significant insights into some of the fundamental biological relationships that have shaped our thinking about the system by exploring the relationship between X2, flow, fish abundance, and the low salinity zone.


Through modeling, it has been possible to move beyond salinity to understand how large-scale changes to the system are likely to affect sediment dynamics, and to assess the potential effects on species that rely on turbidity for habitat. Lastly, the coupling of multi-dimensional hydrodynamic models with particle tracking models has led to advances in our thinking about residence time, the retention of food organisms, the effect of south Delta exports on larval entrainment, and the pathways and behaviors of salmonids that travel through the Delta.


This chapter provides an overview of these recent advances and how they have increased our understanding of the distribution and movement of fish and food organisms. The applications presented serve as a guide to the current state of the science of Delta modeling and provide examples of how we can use multidimensional models to predict how future Delta conditions will affect both fish and water supply.


Read the full chapter here



Factors and Processes Affecting Delta Levee System Vulnerability

The authors appraised factors and processes related to human activities and high water, subsidence, and seismicity. Farming and drainage of peat soils over time has caused a gradual sinking which contributed to internal levee failures. Although these subsidence rates have decreased with time, they still contribute to levee instability. Additional data is needed to assess spatial and temporal effects of subsidence caused by peat thinning and deformation. Since the mid-1970s large-scale, State investments in levee upgrades have increased conformance, however accounts continue to conflict on how these investments correspond to the numbers of failures.


Both modeling and history suggest that the projected increases of high-flow frequency associated with climate change will increase levee-failures rates. Quantification of this increased threat requires further research. A reappraisal of seismic threats resulted in updated ground motion estimates for multiple faults and earthquake occurrence frequencies. The immediate seismic threat, liquefaction, is the sudden loss of strength due to an increase in the pressure of the pore fluid and corresponding loss of contact forces. However, levees damaged during an earthquake that do not immediately fail, may eventually breach.


Consequences for future levee failure are estimated to cost up to billions of dollars. The analysis of future risks will benefit from more detailed descriptions of levee strength and upgrades, consideration of subsidence, climate change, and earthquake threats. Ecosystem benefits of levee habitats in this highly altered system are thin. Better recognition and coordination is needed among the creation of high value habitats, levee needs, costs, benefits of levee improvements, and breaches.   


Read the full chapter here



Nutrient Dynamics of the Delta: Effects on Primary Producers

Increasing clarity of Delta waters, the emergence of harmful algal blooms, the growth of aquatic water weeds, and the altered food web of the Delta have recently brought nutrient dynamics to the forefront. This paper focuses on the sources of nutrients, the transformation and uptake of nutrients, and the links of nutrients to primary producers.


The largest loads of nutrients to the Delta come from the Sacramento River with the San Joaquin River seasonally important, especially in the summer. Light regime, grazing pressure, and nutrient availability influence rates of primary production at different times and locations within the Delta. Modern sensor technology and networks are now deployed that make high frequency measurements of nitrate, ammonium, and phosphate. Data from such instruments allow a much more detailed assessment of the spatial and temporal dynamics of nutrients.


Four fruitful directions for future research include utilizing continuous sensor data to estimate rates of primary production and ecosystem respiration, linking models of the Delta with the transport and fate of dissolved nutrients, studying nutrient dynamics in various habitat types, and exploring the use of stable isotopes to trace the movement and fate of effluent-derived nutrients.


Read the full chapter here



Contaminant Effects on California Bay-Delta Species & Human Health

Many contaminants in the California Bay-Delta exceed regulatory standards, impact aquatic species, and potentially affect human health. Recent studies provide evidence that contaminants impact species of concern in the Bay-Delta (e.g., the decline of several important fish species referred to as the “Pelagic Organism Decline”). Multiple chemicals impair processes at cellular and physiological levels (measured as growth, development, and behavior abnormalities), ultimately affecting populations.


As an important example, the population decline of the endangered delta smelt (Hypomesus transpacificus) is significantly associated with multiple stressors, including insecticide use. New analyses presented in this paper show significant correlations between pyrethroid (an insecticide) use and declining abundance of POD fish species.


Water sampled from the Bay-Delta causes multiple harmful effects in fish and delta smelt. Fish prey items are also impacted by contaminants; this may have an indirect effect on their populations. Co-occurrence with thermal changes or disease can worsen contaminant effects.


Contaminants also pose threats to human health via consumption of fish, drinking water, and contact recreation, in particular, mercury, toxins, disinfection byproducts, pesticides, pharmaceuticals, and personal care products. The role of contaminants in the decline of Bay-Delta species is difficult to accurately assess in a complex, dynamic system. However, tools and approaches are available to evaluate contaminant impacts on Bay-Delta species, and separate the effects of multiple stressors. Integrated monitoring and focused mechanistic studies are instrumental for addressing management needs. Impact and risk assessments should be conducted for different species across multiple life stages, with emphasis on early life stages of high-priority Bay-Delta species.


Read the full chapter here



Perspectives on Bay–Delta Science and Policy


The State of Bay–Delta Science 2008 highlighted seven emerging perspectives on science and management of the Delta. These perspectives had important effects on policy and legislation concerning management of the Delta ecosystem and water exports. From the collection of papers that make up the State of Bay–Delta Science 2016, the authors derive another seven perspectives that augment those published in 2008. The new perspectives address nutrient and contaminant concentrations in Delta waters, the failure of the Delta food web to support native species, the role of multiple stressors in driving species toward extinction, and the emerging importance of extreme events in driving change in the ecosystem and the water supply.



Despite these new tools and scientific insights, species conservation objectives for the Delta are not being met. The authors believe that this lack of progress stems in part from the fact that science and policy do not incorporate sufficiently long-term perspectives. Looking forward half a century was central to the Delta Visioning process, but science and policy have not embraced this conceptual breadth. The authors are also concerned that protection and enhancement of the unique cultural, recreational, natural resource, and agricultural values of the Delta as an evolving place, as required by the Delta Reform Act, has received no critical study and analysis. Adopting wider and longer science and policy perspectives immediately encourages recognition of the need for evaluation, analysis, and public discourse on novel conservation approaches. These longer and wider perspectives also encourage more attention to the opportunities provided by heavily invaded ecosystems. It is past time to turn scientific and policy attention to these issues.


Read the full chapter here



Summary for Policymakers

Delta science needs to push beyond its tendency to focus on short-term policy mandates and near-term crises. Taking a longer, 50- to 100-year viewpoint has been part of various planning exercises including Delta Vision. That kind of long-range thinking now needs to be more strongly incorporated into the whole Delta science and management endeavor. An appreciation of the changes that are coming, particularly those associated with climate change, needs to inform all our research and planning.


In the meantime, despite management actions that in some instances appear heroic, native fish continue to decline in the Delta. The food web has changed dramatically, new stressors are added daily to existing ones, and several native species are virtually extinct. While we must continue to try to shore up the delta smelt, for example, it is time for serious debate about more radical alternatives to habitat restoration, including assisted relocation, assisted evolution, even perhaps cryopreservation (freezing of genetic materials). Agency mandates based on the past should not prevent us from taking actions that prepare us for a very different future.


The capacity of the Delta to absorb extremes of all kinds is declining. In the future, water managers will have to adjust to reduced and more variable inflows to the Delta and to less predictable sources of water supply. Sustaining a Delta ecosystem hospitable to native species will be much more difficult. In that case, it may become necessary to refocus on managing for novel plant and animal communities that provide desirable ecosystem services. Delaying action until the next crisis is upon us will greatly increase the risk and costs of failure.


Read the summary here


Coequal goals

The Delta Stewardship Council was created in legislation to achieve the state mandated coequal goals for the Delta. "'Coequal goals' means the two goals of providing a more reliable water supply for California and protecting, restoring, and enhancing the Delta ecosystem. The coequal goals shall be achieved in a manner that protects and enhances the unique cultural, recreational, natural resource, and agricultural values of the Delta as an evolving place." (CA Water Code §85054)