Effects of the South Delta Agricultural Barriers on Emigrating Juvenile Salmonids

California Department of Water Resources (DWR) | November 28th, 2018

The TBP is implemented in compliance with the terms and conditions of two NMFS Biological Opinions (BiOp) (NMFS 2008, 2009). To comply with the requirements of the NMFS

The TBP is implemented in compliance with the terms and conditions of two NMFS Biological Opinions (BiOp) (NMFS 2008, 2009). To comply with the requirements of the NMFS BiOps, a study of the effects of the three SDABs (i.e., ORTB, MRB, and GLCB) on emigrating (i.e., out-migrating) juvenile salmonids was conducted (2010–2011) and the results are reported in this document. There were four effects considered in this study: 1) survival of juvenile salmonids (Ŝ); 2) juvenile salmonid time-in-vicinity (TIV) of a barrier; 3) predation on juvenile salmonids; and 4) predatory fish density evaluations near the barriers before-, during-, and after- construction during each study year. For one barrier, the ORTB, two-dimensional (2D) acoustic fish tracks for juvenile salmonids were used to evaluate: 1) the rates of successful passage through the barrier; and 2) route selection through the barrier. In addition, utilizing the ORTB 2D fish tracks for both juvenile salmonids and predatory fish, a mixture model (Romine et al. 2014) approach was employed to determine the probability that a juvenile salmonid had been eaten by a predatory fish in the vicinity of the ORTB.

Effects of Tidal Wetland Restoration on Fish: A Suite of Conceptual Models

California Department of Water Resources (DWR) | November 2nd, 2017

Fishes native to the Sacramento-San Joaquin Delta and Suisun Marsh have historically had access to a complex mosaic of dendritic channels, large tule marshes, floodplain

Fishes native to the Sacramento-San Joaquin Delta and Suisun Marsh have historically had access to a complex mosaic of dendritic channels, large tule marshes, floodplains, and riparian woodlands. After the Gold Rush, that habitat was rapidly and drastically altered, and today several native fish species occur in record low numbers. Although many other stressors also contributed to population declines, habitat restoration is a major component of strategies to reverse the trend. Programs such as the Fish Restoration Program particularly emphasize restoration of tidal wetlands and associated shallow subtidal habitat and strive to restore and learn in an adaptive management context. Conceptual models, therefore, are necessary to plan both the restoration and the monitoring and evaluation of restoration actions.

Effects of Tidally Varying River Flow on Entrainment of Juvenile Salmon into Sutter and Steamboat Sloughs

University of California, Davis (UC Davis) | June 1st, 2021

Survival of juvenile salmonids in the Sacramento–San Joaquin Delta (Delta) varies by migration route, and thus the proportion of fish that use each route affects overal

Survival of juvenile salmonids in the Sacramento–San Joaquin Delta (Delta) varies by migration route, and thus the proportion of fish that use each route affects overall survival through the Delta. Understanding factors that drive routing at channel junctions along the Sacramento River is therefore critical to devising management strategies that maximize survival. Here, we examine entrainment of acoustically tagged juvenile Chinook Salmon into Sutter and Steamboat sloughs from the Sacramento River. Because these sloughs divert fish away from the downstream entrances of the Delta Cross Channel and Georgiana Slough (where fish access the low-survival region of the interior Delta), management actions to increase fish entrainment into Sutter and Steamboat sloughs are being investigated to increase through-Delta survival. Previous studies suggest that fish generally “go with the flow”—as net flow into a divergence increases, the proportion of fish that enter that divergence correspondingly increases. However, complex tidal hydrodynamics at sub-daily time-scales may be decoupled from net flow. Therefore, we modeled routing of acoustic tagged juvenile salmon as a function of tidally varying hydrodynamic data, which was collected using temporary gaging stations deployed between March and May of 2014. Our results indicate that discharge, the proportion of flow that entered the slough, and the rate of change of flow were good predictors of an individual’s probability of being entrained. In addition, interactions between discharge and the proportion of flow revealed a non-linear relationship between flow and entrainment probability. We found that the highest proportions of fish are likely to be entrained into Steamboat Slough and Sutter Slough on the ascending and descending limbs of the tidal cycle, when flow changes from positive to negative. Our findings characterize how patterns of entrainment vary with tidal flow fluctuations, providing information critical for understanding the potential effect of management actions (e.g., fish guidance structures) to modify routing probabilities at this location.

Effects of vegetation on methylmercury concentrations and loads in a mercury contaminated floodplain

Science of The Total Environment (Elsevier) | August 3rd, 2023

The Yolo Bypass (YB) is a large flood conveyance system designed to protect the city of Sacramento, California, USA from flooding when the Sacramento River approaches flo

The Yolo Bypass (YB) is a large flood conveyance system designed to protect the city of Sacramento, California, USA from flooding when the Sacramento River approaches flood stage. The Sacramento River watershed and YB are a source of methylmercury (MeHg) to downstream habitat as a result of historic mercury (Hg) and gold mining practices. In the dry season, the YB is extensively farmed and grazed. However, depending on the water year, the floodplain may remain inundated for months. Our experiments focused on the role of pasture land and decomposing vegetation as a source of MeHg during extensive periods of floodplain flooding. Decomposing vegetation, rather than sediment, was identified as the principal source of filter passing MeHg (fMeHg) within the floodplain. The decomposing vegetation provided a substrate for microbial methylation of inorganic Hg contained within the plants. In replicated flooded mesocosm experiments, MeHg concentrations increased from 2.78 to 31.0 ng g− 1 dw and 3.41 to 56.8 ng g− 1 dw in decomposing vegetation. In field collections, the concentrations of MeHg in vegetation increased from preflood levels of 2.78 to 45.4 ng g− 1dw after 17 weeks of flooding. The importance of vegetation was shown in laboratory experiments where there was a positive correlation between the amount of fMeHg in water and the amount of vegetation added. These results also provide Hg concentration data for an important functional type of vegetation, grasses, and fill a data gap that contributed to uncertainties with regards to the role of vegetation in Hg cycling.

Elevation and Opportunity in the Delta: Restoring the Right Thing in the Right Place

San Francisco Estuary Institute (SFEI) | May 31st, 2022

A future Sacramento-San Joaquin Delta and Suisun Marsh (“Delta” herein) that supports healthy ecosystems and native species, while also meeting flood risk reduction,

A future Sacramento-San Joaquin Delta and Suisun Marsh (“Delta” herein) that supports healthy ecosystems and native species, while also meeting flood risk reduction, water supply, water quality, carbon sequestration, economic, and cultural objectives, requires that appropriate restoration and management actions be taken in the right place at the right time. Geographic setting affects the potential opportunities available—not all actions are suitable everywhere. Physical factors determining what types of activities are appropriate now and in the future include a site’s elevation, degree of tidal and fluvial influence, salinity, soil type, and local effects of climate change, which all vary spatially across the Delta. While there has been considerable progress over the last several decades, continued acceleration of the pace and scale of enhancement actions appropriate to landscape position is needed. Understanding the physical template is necessary for developing strategies that move beyond opportunistic restoration, support resilience over time, and have the potential to connect and magnify benefits across the larger landscape.

Emergency Drought Barriers

Delta Stewardship Council (Delta Council) | April 26th, 2022

Emergency Response To Flood Threats in California

California Department of Water Resources (DWR) | April 8th, 2011

An explanatory memo on the Flood Operations Branch, Department of Water Resources, Division of Flood Management During the flood season, a number of public agencies co

An explanatory memo on the Flood Operations Branch, Department of Water Resources, Division of Flood Management During the flood season, a number of public agencies combine their efforts to provide high water warnings and minimize flood damage in California. The Department of Water Resources (DWR) is responsible for coordinating local, State and federal flood operations. The State-Federal Flood Operations Center, located on El Camino Avenue in Sacramento, is the focal point of this effort. State, federal and local flood operations on the North Coast streams are coordinated through the DWR Eureka Flood Center in Humboldt County.

Emerging PFAS Trends in Water and Sediment from San Francisco Bay

San Francisco Estuary Institute (SFEI) | August 14th, 2025

Per- and polyfluoroalkyl substances (PFAS) are a diverse class of persistent compounds, including several that are bioaccumulative and known or suspected to be toxic. The

Per- and polyfluoroalkyl substances (PFAS) are a diverse class of persistent compounds, including several that are bioaccumulative and known or suspected to be toxic. These unique compounds have widespread uses across consumer, commercial, and industrial products, resulting in widespread occurrence in humans, the environment, and wildlife across the globe. Within San Francisco Bay, the RMP has monitored PFAS across the Bay ecosystem, beginning in 2004 with various biota and since expanding to sediment, surface water, stormwater, and wastewater. These studies found PFAS throughout the Bay, especially in sport fish, where concentrations are of potential concern for human health and led to a classification of PFAS as High Concern for the Bay under the RMP tiered risk-based framework for emerging contaminants.  This study examined Bay sediment and surface water to continue to build our understanding of the occurrence, fate, and risks of PFAS to ecological and human health. Using a targeted method, 40 PFAS were analyzed in Bay sediment collected in three monitoring cruises from 2017 to 2023, and Bay water collected from 2021 to 2023 during both the dry and wet seasons. The Total Oxidizable Precursor (TOP) assay was also used to supplement these findings by indirectly measuring unknown perfluoroalkyl acid (PFAA) precursors of detectable PFAS. This additional information aids in elucidating the broader levels of PFAS present in samples to better evaluate the exposure and risk to the Bay. 

Empirical and Experimental Analyses of Secondary Louver Efficiency at the Tracy Fish Collection Facility: March 1996 to November 1997

U.S. Bureau of Reclamation (USBR) | January 30th, 2004

Endangered and Threatened Species: Status for the San Francisco Bay-Delta Distinct Population Segment of the Longfin Smelt

U.S. Fish and Wildlife Service (FWS) | February 27th, 2023