The Sacramento-San Joaquin Delta has long been the subject of intensive study.

Yet, not all of these studies have incorporated or proposed good science. Further, resource managers have only sporadically incorporated findings from the best science into the design and implementation of management actions intended to protect and restore the ailing estuary.

Many of the most pressing Delta stressors remain largely unaddressed after a decade and a half of targeted efforts by multiple federal and state agencies. It is essential that sound science is available to regulators, because state and federal agencies are required to utilize the “best available science” in their decision making process.  These decisions often have far reaching impacts on all corners of California, including the Delta.

One prime example is the implementation of the federal Endangered Species Act. If State and Federal agencies are to make effective regulatory decisions, develop responsive species recovery plans, and design effective restoration efforts – sound science is essential.

To achieve this, the Coalition for a Sustainable Delta supports regulatory actions which follow the following recommendations:

• Are spatially explicit, presenting information in the form of maps that reflect geographic variation and site-specific environmental conditions;
• Confronts proposed management actions with available data;
• Are clear on assumptions and uncertainties that affect the management decisions being considered, clearly stating limitations of findings;
• Are set in an appropriate geographic region in order to address the ecological challenge at hand;
• Takes advantage of all available pertinent information, including previous work that both supports and does not support the best judgment of resource managers, and attempts to explain discrepancies;
• Ranks or grades available information, based on the reliability of its sources (published, unpublished, agency publications, etc.);
• Relies on modeling of specific species, their habitats and ecosystems, and the full range of stressors that affect them;
• Uses analytical tools appropriate to the conservation challenge being confronted;
• Uses a structured approach to an effects analysis (or risk assessment); and
• Employs a rigorous specification of response and environmental variables in any analyses used to guide management or policy decisions.

In addition, Guidance on the Use of Best Available Science under the U.S. Endangered Species Act by Dennis D. Murphy and Paul S. Weiland, provides analysis of the challenges met in providing the best available science to Endangered Species Act decision making.

Recommended Resources:

Coalition for a Sustainable Delta: Reconsidering the Fall X2 Action Using the Best Available Scientific Information (2018)

These findings indicate that the evidence presented in the 2008 biological opinion and relied upon by the U.S. Fish and Wildlife Service does not support the assertion that there is a relationship between X2 and heighted performance – abundance and/or subsequent reproductive success – of delta smelt. 

Joseph E. Merz, Paul S. Bergman, Joseph L. Simonis, David Delaney, James Pierson, Paul Anders: Long-Term Seasonal Trends in the Prey Community of Delta Smelt (Hypomesus transpacificus) Within the Sacramento-San Joaquin Delta, California (2016)

We present the first evidence of a shift in the timing of peak abundance for zooplankton species that are key prey items of delta smelt, a federally threatened pelagic fish species. These timing shifts may have exacerbated well-documented food limitations of delta smelt due to declines in primary productivity since the invasion of the overbite clam. 

William Miller, Bryan Manly, Dennis Murphy, David Fullerton, Rob Roy Ramey: An Investigation of Factors Affecting the Decline of Delta Smelt in the Sacramento-San Joaquin Estuary (2012)

Three questions are addressed here: What is the relative importance of environmental factors with direct effects on abundance? Do factors that may have indirect effects provide an explanation of abundance changes? Are effects of environmental factors better accounted for individually or as criteria defining the volume of water with suitable abiotic attributes?

Alexander Parker , Richard Dugdale, Frances Wilkerson: Elevated ammonium concentrations from wastewater discharge depress primary productivity in the Sacramento River and the Northern San Francisco Estuary (2012)

These findings indicate that increased anthropogenic ammonium may decrease estuarine primary production and increase export of ammonium to the coastal ocean.

Alexander Parker, Victoria Hogue, Frances Wilkerson, Richard Dugdale: The effect of inorganic nitrogen speciation on primary production in the San Francisco Estuary(2012)

Historical changes in wastewater practices have increased the proportion of ammonium to the DIN pool in the San Francisco Estuary  leading to reduced access to nitrate by phytoplankton. This may help to explain some of the reduced primary production and phytoplankton biomass observed there since the 1970s.

Patricia Glibert,University of Maryland: Ecological stoichiometry and its implications for aquatic ecosystem sustainability (2011)

Multiple feedbacks serve to alter food web structure when nutrient loads are altered. Such feedbacks may also lead to conditions conducive to invasive species and altered stable states as illustrated for the San Francisco Bay Delta and the Rhine River.

Mark Maunder, Richard Deriso: A state–space multistage life cycle model to evaluate population impacts in the presence of density dependence: illustrated with application to delta smelt (2011)

Our results indicate that density dependence and a few key factors impact the delta smelt population. Temperature, prey, and predators dominated the factors supported by the data and operated on different life stages. The included factors explain the recent declines in delta smelt abundance and may provide insight into the cause of the pelagic species decline in the San Francisco Estuary.

Dennis Murphy, Paul Weiland, Kenneth Cummins: A Critical Assessment of the Use of Surrogate Species in Conservation Planning in the Sacramento-San Joaquin Delta (2011)

Wildlife managers and policy makers have adopted the surrogate species concept, reflecting the limited information available on most species at risk of extirpation or extinction and constraints on resources available to support conservation efforts. Recently developed validation procedures may allow for the productive use of surrogates in conservation planning, but, used without validation, the surrogate species concept is not a reliable planning tool.

Joseph E. Merz, Scott Hamilton, Paul S. Bergman, Bradley Cavallo: Spatial perspective for delta smelt a summary of contemporary survey data(2011)

This comprehensive review provides managers and scientists an improved depiction of the spatial and temporal extent of the delta smelt throughout its range and lends itself to future analysis of delta smelt population assessment and restoration planning.

David Schoellhamer: Sudden Clearing of Estuarine Waters upon Crossing the Threshold from Transport to Supply Regulation of Sediment Transport as an Erodible Sediment Pool is Depleted: San Francisco Bay, 1999 (2010)

The quantity of suspended sediment in an estuary is regulated either by transport, where energy or time needed to suspend sediment is limiting, or by supply, where the quantity of erodible sediment is limiting. This paper presents a hypothesis that suspended-sediment concentration in estuaries can suddenly decrease when the threshold from transport to supply regulation is crossed as an erodible sediment pool is deplete.

Heather Peterson, Marc Vayssieres: Benthic Assemblage Variability in the Upper San Francisco Estuary: A 27-Year Retrospective(2010)

We conclude that the continuity of benthic assemblages and community metrics along the salinity gradient is a powerful and necessary context for understanding historical variability in assemblage composition at geographically static monitoring stations.

James thomson, Wim Kimmerer, Lary Brown, et al.: Bayesian change point analysis of abundance trends for pelagic fishes in the upper San Francisco Estuary (2010)

We examined trends in abundance of four pelagic fish species (delta smelt, longfin smelt, striped bass, and threadfin shad) in the upper San Francisco Estuary, over 40 years using Bayesian change point models.  There were step declines in abundances of all four species in the early 2000s, with a likely common decline in 2002. Abiotic variables, including water clarity, position of the 2% isohaline (X2), and the volume of freshwater exported from the estuary, explained some variation in species’ abundances over the time series, but no selected covariates could explain statistically the post-2000 change points for any species.

James Hobbs, Levi Lewis, Naoaki Ikemiyagi, Ted Sommer, Randall Baxter: The use of otolith strontium isotopes to identify nursery habitat for a threatened estuarine fish (2010)

Our results indicate that otolith strontium isotopes are a powerful tool for identifying nursery habitats for estuarine fishes.  Low salinity habitats disproportionally contributed more recruits relative to both freshwater and brackish water habitats and, therefore, may function as important nursery areas. Furthermore, the relative importance of the low salinity zone to successful recruitment appeared greatest in years following the longfin smelt population decline.

Patricia Glibert, University of Maryland: Long-term Changes in Nutrient Loading and Stoichiometry and their Relationships with Changes in the Food Web and Dominant Pelagic Fish Species in the San Francisco Estuary, California (2010)

This analysis tests the hypothesis that changes in nutrient loads, imbalances in nitrogen: phosphorus, and changes in nitrogen form, especially shifts to increasing loads of chemically reduced, rather than oxidized nitrogen, can have major impacts on food webs, from primary producers through secondary producers to fish.

Ralph McNally, James Thomson, Wim Kimmerer, et al.: Analysis of pelagic species decline in the upper San Francisco Estuary using multivariate autoregressive modeling (2010)

Four species of pelagic fish of particular management concern in the upper San Francisco Estuary, California, USA, have declined precipitously since ca. 2002: delta smelt, longfin smelt, striped bass, and threadfin shad. Our application of the MAR model provides evidence from a multivariate analysis of how abiotic habitat factors directly relate to declining fish abundance in the upper San Francisco Estuary and indirectly to these fish populations through the food web.

Maxine Wright-Walters, Conrad Volz:  Municipal wastewater concentrations of pharmaceutical and xeno-estrogens: Wildlife and human health implications(2009)

Understanding the species and xenoestrogen concentrations in surface water is imperative for environmental public health tracking of associated disease states. Such research will determine the necessity for utilizing limited and competing public financial resources to invest in technology to remove xenoestrogens from surface waters and, in regulation of fish or wildlife consumption from our rivers and lakes.

Wim Kimmerer, Edward Gross, Michael L. MacWilliams: Is the Response of Estuarine Nekton to Freshwater Flow in the San Francisco Estuary Explained by Variation in Habitat Volume? (2009)

In this paper, we determine how the quantity of habitat for estuarine nekton, defined by salinity and water depth, responds to changes in freshwater flow in the San Francisco Estuary and the extent to which species-specific habitat responses translate to flow responses. 

Ken Cummins, Chris Furey, Albert Giorgi, et al.: Listen to the River: An Independent Review of the CVPIA Fisheries Program (2008)

Underlying this independent review of the CVPIA anadromous fish program, asked for by the federal agencies, is the question why the CVPIA program has not been successful in achieving its mission. In this report, we identify scientific, institutional and programmatic obstacles to the success of the CVPIA, drawing conclusions from the information provided. 

Steven Lindley, Robert Schick, Ethan Mora, et al.: Framework for Assessing Viability of Threatened and Endangered Chinook Salmon and Steelhead in the Sacramento-San Joaquin Basin (2007)

In spite of the precarious position of Central Valley salmonid ESUs, there are prospects for greatly improving their viability. Recovering Central Valley ESUs may require re-establishing populations where historical populations have been extirpated (e.g., upstream of major dams). Such major efforts should be focused on those watersheds that offer the best possibility of providing suitable habitat in a warmer future. 

Wim Kimmerer, Dennis Murphy and Paul Angerme: A Landscape level Model for Ecosystem Restoration in the San Francisco Estuary and its Watershed (2005)

We believe CALFED and other large restoration programs will be most successful if they are able to integrate both societal expectations and scientific study at the landscape level.

William Bennett, UC Davis: Critical Assessment of the Delta Smelt Population in the San Francisco Estuary, California (2005)

Overall, a better understanding of the life history, habitat requirements, and limiting factors will be essential for developing tools for management and restoration.  therefore, given the implications for managing California water supply and the current state of population abundance, a good investment would be to fill the critical data gaps outlined here through a comprehensive program of research.

Wim Kimmerer, San Francisco State University: Open Water Processes of the San Francisco Estuary: From Physical Forcing to Biological Responses (2004)

This paper reviews the current state of knowledge of the open waters of the San Francisco Estuary. Opportunities for restoration in the open waters of the estuary are somewhat limited by the lack of scientific basis for restoration, and the difficulty in detecting ecosystem responses in the context of high natural variability.

Larry Brown, U.S. Geological Survey: Will Tidal Wetland Restoration Enhance Populations of Native Fishes?(2003)

Will tidal wetland restoration enhance populations of native fishes? Constructing the conceptual models and evaluating the questions identify important areas of scientific uncertainty.  These uncertainties suggest an array of methods to reduce uncertainty in assessing the benefits of wetland restoration to native fishes.

Paciencia Young, Joseph Cech Jr: Environmental Tolerances and Requirements of Splittail  (1996)

The range of splittail PogolliciJlhys macro/epidollls has decreased to less than a third of its original range due to loss or alteration of habitats. A lack of sufficient flooded vegetation for spawning and rearing. narrower environmental tolerances of other life stages (i.e .. eggs. larvae. and adult spawners). or biotic factors (e.g., predation. competition) may be limiting splittail abundance and distribution. 

Stephen Monismith, Jon Burau, Mark Stacey: Stratification dynamics and gravitational circulation in Northern San Francisco Bay(1996)

Results suggest that there exists a critical condition where tidal mixing is unable to overcome the creation of stratification by advection.

James Orso and Walter Mecum, California Department of Fish & Game: Food limitations as the probable cause of a long-term decline in the abundance of neomysis mercedis (the opossum shrimp) in the Sacramento-San Joaquin estuary(1996)

Five hypotheses for the decline were investigated: (1) reduced concentration by estuarine gravitational flow and increased seaward loss to tidal pumping, (2) food limitation, (3) rice herbicides, (4) high temperature, (5) export pumping losses. Food limitation of juveniles in the form of reduced phytoplankton concentrations best explained the decline. Food appears to be permanently limited by the grazing of the introduced Asian clam. Competition for food by two introduced Asian mysid shrimps may also hamper the recovery of the native mysid population. 

Alan Jassby, William Kimmerer, Stephen Monismith, Charles Armor, James Cloern, Thomas Powell, Jerry Schubel, Timothy Vendlinski: Isohaline position as a habitat indicator for estuarine populations (1995)

Populations of native and introduced aquatic organisms in the San Francisco Bay/Sacramento San Joaquin Delta Estuary (“BayJDelta”) have undergone significant declines over the past two decades. Decreased river inflow due to drought and increased freshwater diversion have contributed to the decline of at least some populations. Effective management of the estuary’s biological resources requires a sensitive indicator of the response to freshwater inflow that has ecological significance, can be measured accurately and easily, and could be used as a “policy” variable to set standards for managing freshwater inflow. Positioning of the 27~0 (grams of salt per kilogram of seawater) bottom salinity value along the axis of the estuary was examined for this purpose. 

Andrea E. Alpine and James E. Cloern: Trophic interactions and direct physical effects control phytoplankton biomass and production in an estuary (1992)

These observations support the hypothesis that seasonal and interannual fluctuations in estuarine phytoplankton biomass and primary production can be regulated jointly by direct physical effects (e.g. river-driven transport) and trophic interactions (episodes of enhanced grazing pressure by immigrant populations of benthic suspension feeders). 

James Carlton, Janet Thompson, Laurence Schemel, Frederic Nichols: Remarkable invasion of San Francisco Bay by the Asian clam Potamocobula amurensis (1990)

The early detection of the appearance and spread of p. amurensis in San Francisco Bay makes this one of the best documented invasion of any estuary in the world.