An Alternative Technique to Quantify the Incidental Take of Listed Anadromous Fishes at the Federal and State Water Export Facilities in the San Francisco Bay-Delta Estuary

National Marine Fisheries Service (NMFS) | July 1st, 2011

An assessment of future tidal marsh resilience in the San Francisco Estuary through modeling and quantifiable metrics of sustainability

Frontiers in Environmental Science (Frontiers) | November 25th, 2022

Quantitative, broadly applicable metrics of resilience are needed to effectively manage tidal marshes into the future. Here we quantified three metrics of temporal marsh

Quantitative, broadly applicable metrics of resilience are needed to effectively manage tidal marshes into the future. Here we quantified three metrics of temporal marsh resilience: time to marsh drowning, time to marsh tipping point, and the probability of a regime shift, defined as the conditional probability of a transition to an alternative super-optimal, suboptimal, or drowned state. We used organic matter content (loss on ignition, LOI) and peat age combined with the Coastal Wetland Equilibrium Model (CWEM) to track wetland development and resilience under different sea-level rise scenarios in the Sacramento-San Joaquin Delta (Delta) of California. A 100-year hindcast of the model showed excellent agreement (R2 = 0.96) between observed (2.86 mm/year) and predicted vertical accretion rates (2.98 mm/year) and correctly predicted a recovery in LOI (R2 = 0.76) after the California Gold Rush. Vertical accretion in the tidal freshwater marshes of the Delta is dominated by organic production. The large elevation range of the vegetation combined with high relative marsh elevation provides Delta marshes with resilience and elevation capital sufficiently great to tolerate centenary sea-level rise (CLSR) as high as 200 cm. The initial relative elevation of a marsh was a strong determinant of marsh survival time and tipping point. For a Delta marsh of average elevation, the tipping point at which vertical accretion no longer keeps up with the rate of sea-level rise is 50 years or more. Simulated, triennial additions of 6 mm of sediment via episodic atmospheric rivers increased the proportion of marshes surviving from 51% to 72% and decreased the proportion drowning from 49% to 28%. Our temporal metrics provide critical time frames for adaptively managing marshes, restoring marshes with the best chance of survival, and seizing opportunities for establishing migration corridors, which are all essential for safeguarding future habitats for sensitive species.

An Evaluation of Juvenile Salmonid Routing and Barrier Effectiveness, Predation, and Predatory Fishes at the Head of Old River, 2009–2012

California Department of Water Resources (DWR) | February 2nd, 2015

The California Department of Water Resources (DWR) and the U.S. Bureau of Reclamation (Reclamation) manage the State Water Project (SWP) and Central Valley Project (CVP),

The California Department of Water Resources (DWR) and the U.S. Bureau of Reclamation (Reclamation) manage the State Water Project (SWP) and Central Valley Project (CVP), respectively, and are charged to do so in a manner that maintains the survival of anadromous salmonids subject to the terms of the National Marine Fisheries Service’s (NMFS) 2009 Biological Opinion (BO) and 2011 amendments regarding the Long-Term Central Valley Project and State Water Project Operations Criteria and Plan (OCAP). Action IV.1.3 of the NMFS’s 2009 BO instructs these agencies to “consider engineering solutions to further reduce diversion of emigrating juvenile salmonids to the interior and southern Delta, and reduce exposure to CVP and SWP export facilities.” Specifically, one objective of Action IV.1.3 is to “prevent emigrating salmonids from entering channels in the south Delta (e.g., Old River, Turner Cut) that increase entrainment risk to Central Valley steelhead migrating from the San Joaquin River through the Delta.”

An Introduction to High-Frequency Nutrient and Biogeochemical Monitoring for the Sacramento– San Joaquin Delta, Northern California

U.S. Geological Survey (USGS) | July 11th, 2017

This report is the first in a series of three reports that provide information about high-frequency (HF) nutrient and biogeochemical monitoring in the Sacramento–San Jo

This report is the first in a series of three reports that provide information about high-frequency (HF) nutrient and biogeochemical monitoring in the Sacramento–San Joaquin Delta of northern California (Delta). This first report provides an introduction to the reasons for and fundamental concepts behind collecting HF measurements, and describes the benefits associated with a real-time, continuous, HF, multi-parameter water quality monitoring station network that is co-located with flow stations. It then provides examples of how HF nutrient measurements have improved our understating of nutrient sources and cycling in aquatic systems worldwide, followed by specific examples from the Delta. These examples describe the ways in which HF instrumentation may be used for both fixed-station and spatial assessments. The overall intent of this document is to describe how HF measurements currently (2017) are being used in the Delta to examine the relationship between nutrient concentrations, nutrient cycling, and aquatic habitat conditions.

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

University of California, Davis (UC Davis) | December 1st, 2016

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 an

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.  

Anadromous Salmonids in the Delta: New Science 2006-2016

University of California, Davis (UC Davis) | July 1st, 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 migrati

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.

Analyses of Rotary Screw Trap Sampling of Migrating Juvenile Chinook Salmon in the Stanislaus River, 1996-2005

Delta Stewardship Council (Delta Council) | August 1st, 2006

Anderson-Cottonwood Irrigation District Integrated Regional Water Management Program – Groundwater Production Element Project

U.S. Bureau of Reclamation (USBR) | August 15th, 2011

This project would improve the flexibility and reliability of the District’s water supply, particularly during dry and critically dry water years. In 2004, ACID’s sur

This project would improve the flexibility and reliability of the District’s water supply, particularly during dry and critically dry water years. In 2004, ACID’s surface water rights were reduced from 165,000 to 121,000 ac-ft per year as part of the renegotiation of the 40-year Settlement Contract. Furthermore, the west side of the District’s system has little to no downstream control. Control of the system is achieved at the head of the 35-mile main canal, causing some delivery difficulties at the downstream end of the service area. By pushing water from upstream to downstream without an ability to manage intermediate water surface elevations, downstream response time to water delivery needs can be greatly hindered. This project would help with the flexibility and reliability required to meet agricultural water needs.

Annual Report of Activities October 1, 2013 to September 30, 2014, American River Group (ARG)

Delta Stewardship Council (Delta Council) | September 30th, 2014

Annual Report of Activities October 1, 2013, to September 30, 2014, Delta Operations for Salmonids and Sturgeon (DOSS) Technical Working Group

Delta Stewardship Council (Delta Council) | October 31st, 2014