Synthesis of Data from High-Frequency Nutrient and Associated Biogeochemical Monitoring for the Sacramento– San Joaquin Delta, Northern California

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

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

This report is the second 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). The purpose of this report is to synthesize the data available from a nutrient and water-quality HF (about every 15 minutes) monitoring network operated by the U.S. Geological Survey in the northern Delta. In this report, we describe the network and focus on the purpose of each station. We then present and discuss the available data, at various timescales—first at the monthly, seasonal, and inter-annual timescales, and second, for comparison, at the tidal and event timescales. As expected, we determined that there is substantial variability in nitrate-N concentrations at short timescales within hours, but also significant variability at longer timescales such as months or years. Resolving this variability is made possible by the HF data, with the largest variability caused by storms, tides, and diel biological processes. Given this large temporal variability, calculations of cumulative nutrient fluxes (for example, daily, monthly, or annual loads) is difficult without HF data. For example, in the Cache Slough, calculation of the annual load without the tidal variability resulted in a 30 percent underestimation of the true annual load value. We conclude that HF measurements are important for accurate determination of fluxes and loads in tidal environments, but, more importantly, provide important insights into processes and rates of nutrient cycling. This report, along with the other two reports of this series (Bergamaschi and others, 2017; Kraus, Bergamaschi, and others, 2017), was drafted in cooperation with the Delta Regional Monitoring Program to help scientists, managers, and planners understand how HF data improve our understanding of nutrient sources and sinks, drivers, and effects in the Delta.

Synthesis of Studies in the Fall Low-Salinity Zone of the San Francisco Estuary, September–December 2011

U.S. Geological Survey (USGS) | July 14th, 2014

In fall 2011, a large-scale investigation (fall low-salinity habitat investigation) was implemented by the Bureau of Reclamation in cooperation with the Interagency Ecolo

In fall 2011, a large-scale investigation (fall low-salinity habitat investigation) was implemented by the Bureau of Reclamation in cooperation with the Interagency Ecological Program to explore hypotheses about the ecological role of low-salinity habitat in the San Francisco Estuary—specifically, hypotheses about the importance of fall low-salinity habitat to the biology of delta smelt Hypomesus transpacificus, a species endemic to the San Francisco Estuary and listed as threatened or endangered under federal and state endangered species legislation. The Interagency Ecological Program is a consortium of 10 agencies that work together to develop a better understanding of the ecology of the Estuary and the effects of the State Water Project and Federal Central Valley Project operations on the physical, chemical, and biological conditions of the San Francisco Estuary. The fall low-salinity habitat investigation constitutes one of the actions stipulated in the Reasonable and Prudent Alternative issued with the 2008 Biological Opinion of the U.S. Fish and Wildlife Service, which called for adaptive management of fall Sacramento-San Joaquin Delta outflow following “wet” and “above normal” water years to alleviate jeopardy to delta smelt and adverse modification of delta smelt critical habitat. The basic hypothesis of the adaptive management of fall low-salinity habitat is that greater outflows move the low-salinity zone (salinity 1–6), an important component of delta smelt habitat, westward and that moving the low-salinity zone westward of its position in the fall of recent years will benefit delta smelt, although the specific mechanisms providing such benefit are uncertain. An adaptive management plan was prepared to guide implementation of the adaptive management of fall low-salinity habitat and to reduce uncertainty. This report has three major objectives: •To provide a summary of the results from the first year of coordinated fall low-salinity habitat studies and monitoring. •To provide a synthesis of the results of the fall low-salinity habitat studies and other ongoing research and monitoring, to determine if the available information supports the hypotheses behind the adaptive management of fall low-salinity habitat as set forth in the adaptive management plan. •To begin to put the results from the fall low-salinity habitat studies into context within the larger body of knowledge regarding the San Francisco Estuary and, in particular, the upper San Francisco Estuary, including the Sacramento-San Joaquin Delta, Suisun Bay, and associated embayments.

Technical Report for the Interagency Ecological Program (IEP) Pelagic Organism Decline (POD) Workgroup: Assessment of Aquatic Herbicide Use in the Delta

San Francisco Estuary Institute (SFEI) | May 15th, 2006

Since 2001, the California Department of Boating and Waterways (DBW) has conducted an extensive water quality monitoring program in conjunction with its aquatic herbicide

Since 2001, the California Department of Boating and Waterways (DBW) has conducted an extensive water quality monitoring program in conjunction with its aquatic herbicide applications. In this report, the risk quotient calculation method utilized by the Aquatic Pesticide Monitoring Program (a USEPA Tier 1 risk assessment) was used to determine if there are patterns of Level of Concern exceedances that indicate the possibility of adverse impacts on the Delta aquatic ecosystem due to DBW aquatic herbicide applications. Level of Concern exceedances are indicative only of the need for further investigation of an application scenario and do not, in and of themselves, indicate adverse impacts. This type of risk analysis cannot quantify the potential additive or synergistic effects of all pelagic organism stressors (one of which would be aquatic herbicides) within the Delta. This risk assessment indicates that, with the exception of diquat dibromide applications, DBW herbicide applications are unlikely to have the potential to cause Delta ecosystem water quality impacts. While there were a number of Level of Concern exceedances for diquat, DBW and all regulatory agencies involved were aware of this potential prior to application. NOAA Fisheries requested that, when possible, diquat used adjacent to salmon migratory routes should be reduced or avoided when that species is likely to be present. USFWS determined that diquat impact to aquatic invertebrates is minimal, temporary, and not likely to jeopardize Delta smelt but has required avoidance in areas where and when the smelt are known to be present. For 2006, NOAA has allowed DBW to treat sites in April and May with fluridone, which has allowed the use of diquat to be discontinued.

Technical Report on Barriers: A part of the comprehensive survey of San Francisco Bay and tributaries, California

U.S. Army Corps of Engineers (USACE) | March 15th, 1963

Technical Report on the Scientific Basis for Alternative San Joaquin River Flow and Southern Delta Salinity Objectives

California State Water Resources Control Board (SWRCB) | February 15th, 2012

The State Water Resources Control Board (State Water Board) is in the process of reviewing the San Joaquin River (SJR) flow objectives for the protection of fish and wild

The State Water Resources Control Board (State Water Board) is in the process of reviewing the San Joaquin River (SJR) flow objectives for the protection of fish and wildlife beneficial uses, water quality objectives for the protection of southern delta agricultural beneficial uses, and the program of implementation for those objectives contained in the 2006 Water Quality Control Plan for the San Francisco Bay/Sacramento-San Joaquin Delta Estuary (2006 Bay- Delta Plan). Figure 1.1 displays the project area corresponding to SJR flow objectives and program of implementation and Figure 1.2 displays the project area for the southern Delta water quality objectives and program of implementation. The information and analytical tools described in this report (referred to hereafter as Draft Technical Report or Technical Report) are intended to provide the State Water Board with the scientific information and tools needed to consider potential changes to these objectives and their associated program of implementation. In this quasi-legislative process, State Water Board staff will propose amendments to the SJR flow objectives for the protection of fish and wildlife beneficial uses, southern Delta water quality objectives for the protection of agricultural beneficial uses, and the program of implementation contained in the 2006 Bay-Delta Plan. Also, the environmental impacts of these amendments will be evaluated in a Substitute Environmental Document (SED) in compliance with the California Environmental Quality Act. Any changes to water rights consistent with the revised program of implementation will be considered in a subsequent adjudicative proceeding.

Technical Review of the Draft Staff Report/Substitute Environmental Document in Support of Potential Updates to the Water Quality Control Plan and Associated Modeling

Northern California Water Association (NCWA) | January 18th, 2024

Technical Workshop on Estuarine Habitat in the Bay Delta Estuary

San Francisco Estuary Institute (SFEI) | March 27th, 2012

The Technical Workshop on Estuarine Habitat in the Bay Delta Estuary was initiated by U.S. Environmental Protection Agency (EPA), with support from the Aquatic

The Technical Workshop on Estuarine Habitat in the Bay Delta Estuary was initiated by U.S. Environmental Protection Agency (EPA), with support from the Aquatic Science Center (ASC), to obtain scientific input needed to inform EPA on California’s Comprehensive Review of the 2006 Water Quality Control Plan for the Bay Delta Estuary. Gathering a number of recognized experts on the hydrology and ecology of the Bay Delta was an efficient way to hear current knowledge on estuarine habitat, tools for modeling and assessing conditions, and how biological indicators and ecological processes respond to movement of the low salinity zone.  More specifically, the purpose of the workshop was to: Increase our collective understanding about the attributes of estuarine habitat, and the tools we have for protecting it Characterize the response of biological indicators and ecological processes to changing locations of the low salinity zone (LSZ) Generate scientific information that EPA and others can translate into recommendations that support the State’s Comprehensive Review of the 2006 Water Quality Control Plan (WQCP) for the Bay Delta Estuary The following sections describe planning for the workshop and the workshop process itself. The workshop summary condenses the input from participants during the small workgroup sessions and the final plenary session. It captures the breadth of opinions, judgments, and viewpoints expressed without attempting to fact check statements, or reconcile / synthesize disagreements or contradictions. Finally, the facilitator’s report provides my personal impressions of the workshop and the degree to which it achieved its stated purposes.

Technologies for Passing Fish at Large Dams

California Department of Water Resources (DWR) | June 1st, 2013

Given the possible conditions that may exist in Central Valley streams as the climate warms, many researchers and agencies have recognized the need to evaluate opportunit

Given the possible conditions that may exist in Central Valley streams as the climate warms, many researchers and agencies have recognized the need to evaluate opportunities to provide Central Valley salmonid species access to currently inaccessible habitat (DWR 2008, NMFS 2009, and CA Resources Agency 2009). In addition, Lindley et al. (2007) stated that in order to recover Central Valley salmonids, some populations will need to be established in areas now blocked by dams. “The state should work with dam owners and operators, federal resource management agencies, and other stakeholders to evaluate opportunities to introduce or reintroduce anadromous fish to upper watersheds. Reestablishing anadromous fish, such as salmon, upstream of dams may provide flexibility in providing cold water conditions downstream, and thereby help inform system reoperation.” (CA Resources Agency 2009) The U.S. Bureau of Reclamation dedicates over 1.2 million acre-feet of water, through operation of the Central Valley Project, to fish and wildlife. DWR releases water to meet minimum flow and temperature requirements downstream of Oroville Dam. Climate change may warm rivers and streams, with less water available for ecosystem flow and temperature needs in spring and summer (CA Resources Agency 2009). As temperatures warm, more cold water storage may be needed so that releases can be made to meet temperature requirements downstream. Providing anadromous1 fish passage to areas upstream of reservoirs could eliminate or reduce the need for cold water releases and give water managers additional flexibility in meeting downstream water supply and flood protection needs. In addition, it is prudent to consider fish passage opportunities as part of potential systems reoperations because other agencies are conducting planning efforts for fish passage ...

Temporary Urgency Change Petition for February 1, 2023, through March 31, 2023

California State Water Resources Control Board (SWRCB) | February 13th, 2023

Ten Rivers in America's Future, No. 2. The Central Valley of California

U.S. Water Resources Policy Commission | July 1st, 1950