Extensive research shows that factors including invasive species, salinity, and wastewater discharges have harmful effects on the complex ecosystems found in the Delta.

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.

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.

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, 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.

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.

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.