San Francisco Bay Interim Model Validation Report

San Francisco Estuary Institute (SFEI) | December 1st, 2017

As part of the Nutrient Management Strategy, a coupled hydrodynamic-biogeochemical model of San Francisco Bay is being developed. The process-based, numerical model will

As part of the Nutrient Management Strategy, a coupled hydrodynamic-biogeochemical model of San Francisco Bay is being developed. The process-based, numerical model will be used to inform nutrient management decisions, by: • improving quantitative understanding of processes that shape current conditions, • forecasting ecosystem response under future scenarios, and • evaluating potential effectiveness of management actions. This report describes the model in its present configuration and the status of its validation. Model development is necessarily an iterative process, with early stages focused on refining the model’s representation of hydrodynamics and transport, and later stages of the effort including increasingly complex representations of biogeochemistry. Present validation efforts focus on assessing model skill with respect to hydrodynamics, salinity and transport. The final report will additionally consider model validation of water quality and biogeochemical processes.

San Francisco Bay Triennial Bird Egg Monitoring Program for Contaminants, California—2018

U.S. Geological Survey (USGS) | May 23rd, 2019

The Regional Monitoring Program for Water Quality in San Francisco Bay (RMP), administered by the San Francisco Estuary Institute, is a large-scale effort to monitor cont

The Regional Monitoring Program for Water Quality in San Francisco Bay (RMP), administered by the San Francisco Estuary Institute, is a large-scale effort to monitor contaminant trends in water, sediment, fish, and birds throughout San Francisco Bay (San Francisco Estuary Institute, 2016). As part of the RMP and the U.S. Geological Survey (USGS) long-term Wildlife Contaminants Program, the USGS samples double-crested cormorant (Phalacrocorax auritus) and Forster’s tern (Sterna forsteri) eggs throughout the San Francisco Bay approximately every 3 years to assess temporal trends in contaminant concentrations. This sampling has previously been carried out by USGS in 2009, 2012, and 2016. This document summarizes egg collections for 2018, as well as mercury concentrations in Forster’s tern eggs on an individual egg basis. These data are available in a USGS data release (Ackerman and others, 2019).

San Francisco Bay: A Freshwater Starved Estuary

Bay Institute | September 1st, 2016

How Reducing Flows Harms the Ecosystems of San Francisco Bay and Coastal Waters The Bay Institute’s major new study, San Francisco Bay: The Freshwater – Starved Estu

How Reducing Flows Harms the Ecosystems of San Francisco Bay and Coastal Waters The Bay Institute’s major new study, San Francisco Bay: The Freshwater – Starved Estuary, documents how the ecological health of San Francisco Bay and the nearby ocean is at high risk because large-scale water diversion in the Bay’s watershed severely limits the amount of fresh water that reaches the Bay and alters the timing of that flow. Inflow to the Bay from its Central Valley watershed now averages less than half of what it would be without diversions; in some years just one-third of the runoff makes it to the Bay. The result is a nearly permanent drought for the Bay’s fish, wildlife, and their habitats. This radical alteration creates severe consequences for the Bay and marine ecosystems – and Bay Area residents pay the price. The study shows how unsustainable diversion of the Bay’s freshwater inflow: Dramatically cuts production of fish and shrimp that are the food source for marine mammals, like Orca Whales, and birds; Allows pollutants to accumulate to dangerous levels and encourages blooms of toxic algae; Reduces sediment supply to Bay Area wetlands and beaches; Makes it easier for undesirable non-native species to successfully invade the Bay Estuary. The San Francisco Bay Estuary is created by the mixing of fresh water from the Central Valley’s rivers with salt water from the Pacific Ocean. Dramatically reducing the inflow of fresh water generates cascading effects in the Bay’s watershed, the Bay itself, and coastal ocean waters. The report’s major findings include: On average, since 1975 more than half (53%) of runoff from the Central Valley watershed has been diverted, stored, or exported before it can reach the Bay – and in many years two-thirds or more of the Bay’s inflow is captured; As a result of intensive water diversions, the Bay experiences catastrophically dry years almost half the time (only one “supercritically dry” year occurred naturally between 1975-2014, but the Bay experienced nineteen supercritical years during that period); Numerous unrelated fish species – from sharks to salmon, from sturgeon to smelt – show strong positive correlations with Bay Inflow; many of these species are now endangered, and even commercially viable fisheries are in decline; Predators that feed on flow-dependent fish and shrimp are feeling the pinch – for example, dwindling supplies of Central Valley Chinook salmon may restrict the recovery of the local Orca whale population; Blooms of toxic “algae” (cyanobacteria) are becoming more frequent, and other pollutants are becoming more concentrated, as a result of reductions in freshwater flows from the Bay’s watershed; Bay Area beaches and tidal wetlands are deprived of sediment that was once transported by high river flows. The study reports that local businesses are likely to suffer from the Bay’s continued decline, including those related to commercial fishing and tourism. As our Bay, beaches, wetlands, and fish and wildlife populations deteriorate, the quality of life for many Bay Area residents will also be severely – and perhaps permanently – damaged. The study identifies four important approaches to improving Bay inflows: Update the State’s 21 year old water quality standards for the Bay Estuary to ensure adequate inflow Require all those who divert water destined for the Bay, not just a subset, to contribute their fair share of fresh water to support benefits enjoyed by all Californians Invest in local water supplies around the state including conservation, and recycling, that can generate millions of acre-feet of water and reduce reliance on water diverted from the Estuary and its watershed Coordinate management of flows with wetland and beach restoration to more effectively protect shorelines The study was prepared for the San Francisco Estuary Partnership, a coalition of resource agencies, non-profits, citizens, and scientists working to protect, restore, and enhance water quality and fish and wildlife habitat in and around the San Francisco Bay Delta Estuary, which also provided the majority of funding for the project.

San Francisco Estuary Blueprint 2022

San Francisco Estuary Partnership (SFEP) | September 8th, 2022

In the past few years, the San Francisco Estuary region has confronted epic wildfires, historic rainfall intensity and flooding, and chronic drought. The whiplash of thes

In the past few years, the San Francisco Estuary region has confronted epic wildfires, historic rainfall intensity and flooding, and chronic drought. The whiplash of these events has confirmed that climate change has already begun to impact human and wildlife communities from Sacramento to San Francisco, and beyond. Furthermore, a global COVID-19 pandemic has disrupted regional planning and project implementation everywhere, presenting new challenges to traditional processes and creating an unfamiliar working landscape for resource managers. Finally, the pervasive, horrific violence against Black, Brown, and Asian and Asian-American people has amplified long-term calls for racial justice, galvanizing new commitments to address historic and present inequity through every thread of our social fabric. These events have set the context for the multi-stakeholder process that updates the San Francisco Estuary Blueprint.

San Joaquin River Restoration Program

San Joaquin River Restoration Program | December 13th, 2007

San Joaquin River Restoration Settlement

Congressional Research Service (CRS) | November 9th, 2007

Historically, Central California’s San Joaquin River supported large Chinook salmon populations. Since the Bureau of Reclamation’s Friant Dam on the San Joaquin River

Historically, Central California’s San Joaquin River supported large Chinook salmon populations. Since the Bureau of Reclamation’s Friant Dam on the San Joaquin River became fully operational in the 1940s, much of the river’s water has been diverted for off-stream agricultural uses. As a result, approximately 60 miles of the river bed is dry in most years. Thus, the river no longer supports Chinook salmon populations in its upper reaches. In 1988, a coalition of conservation and fishing groups sued Reclamation (Natural Resources Defense Council v. Rodgers). A U.S. District Court judge has ruled that operation of Friant Dam violates state law because of its destruction of downstream fisheries. Faced with mounting legal fees, uncertainty, and the possibility of dramatic cuts to water diversions, parties negotiated a settlement instead of proceeding to trial. In September 2006, an agreement, commonly called the Settlement, was reached. It calls for new releases of water from Friant Dam to restore fisheries, as well as for efforts to mitigate reductions in off-stream deliveries lost to restoration flows. Congressional authorization and appropriations are required for full Settlement implementation. Legislation based on the Settlement (H.R. 4074, H.R. 24 and S. 27) is pending. Related bills have also been introduced. A key legislative issue is how to finance the Settlement, specifically how to resolve congressional pay-as-you-go (PAYGO) issues. Other challenges are how to achieve the Settlement’s dual goals of fisheries restoration and water management, and how to address concerns of stakeholders not party to the Settlement, without disrupting the negotiated agreement. The amount of water projected for restoration flows and the volume of reduced Friant water deliveries are related, but the relationship would not necessarily be one-for-one. Available estimates for total annual Friant water supplies (including both contract and temporary water) are, on average, 15% to 16% less under the Settlement than under current operations; but such estimates do not account for improvements in water management that might reduce the impact on water users. For three-quarters of water contractors, the reduction would represent a reduction in one of their available sources of water. The impacts of such reductions will vary by contractor depending on the firmness of existing surface water supplies and the reliability of groundwater supplies. How to offset the decrease and who would pay for investments in other water sources and improved efficiency has not been determined. Although the region may benefit from increased recreational expenditures and investment in river restoration activities under the Settlement, studies suggest its largest and mostly negative economic impact would be on the agriculture industry, at least in the short term. In addition, downsteam interests not party to the Settlement have been concerned about increased flooding, groundwater infiltration, and competition with existing federal financial commitments. Nearby communities fear harm to groundwater quantity and quality. Some of these concerns have been addressed in the legislation, but some remain. On the other hand, some communities and interests believe restoration will bring other benefits to the river, such as improved surface water quality in lower San Joaquin River reaches. Ultimate Settlement costs and benefits are very difficult to predict.

San Luis National Wildlife Refuge Complex Final Comprehensive Conservation Plan and Environmental Assessment

U.S. Fish and Wildlife Service (FWS) | July 31st, 2024

This Comprehensive Conservation Plan (CCP) will guide the management of the Merced National Wildlife Refuge (NWR), San Luis NWR and Grasslands Wildlife Management Area (W

This Comprehensive Conservation Plan (CCP) will guide the management of the Merced National Wildlife Refuge (NWR), San Luis NWR and Grasslands Wildlife Management Area (WMA) for the next 15 years. Located in Merced County, California (Figure 1-1), these three units are managed and administered by the San Luis National Wildlife Refuge Complex (the Complex). A fourth unit, the San Joaquin River NWR, is also managed and administered by the Complex but already has a CCP for its management, which was completed in 2006 and amended in 2022. For the sake of this document, the term Complex refers to the San Luis NWR, Merced NWR and Grasslands WMA only. The Complex comprises just four of the 568 refuges that currently make up the U.S. Fish and Wildlife Service (USFWS or the Service) National Wildlife Refuge System (NWRS or Refuge System). The mission of the NWRS is to conserve a network of lands and water for the conservation and management of fish, wildlife and plant resources of the United States for the benefit of present and future generations. As part of the Refuge System, the three units—Merced NWR, San Luis NWR and Grasslands WMA—addressed in this CCP provide important habitat for a unique assemblage of both wetland- (particularly waterfowl and other waterbirds) and upland-dependent wildlife species of California’s Central Valley. This CCP is divided into five chapters: Chapter 1, Introduction and Background; Chapter 2, Comprehensive Conservation Planning Process; Chapter 3, Refuge Resources; Chapter 4, Refuge Management Direction; and Chapter 5, Implementation. Click here for full appendices.

San Luis Obispo Coastkeeper v. Santa Maria Valley Water Conservation District

United States District Court, Central District of California | September 23rd, 2022

San Luis Rey Flood Control Project Whelan Mitigation Site Habitat Restoration Action

U.S. Army Corps of Engineers (USACE) | January 15th, 2014

The U.S. Army Corps of Engineers, Los Angeles District (Corps or Los Angeles District) and City of Oceanside (City) propose to restore southwestern willow flycatc

The U.S. Army Corps of Engineers, Los Angeles District (Corps or Los Angeles District) and City of Oceanside (City) propose to restore southwestern willow flycatcher (Empidonax traillii extimus, flycatcher) habitat along the San Luis Rey River, within the San Luis Rey River Flood Risk Management Project Area, to meet environmental commitments and permit requirements consistent with the Record of Decision signed by the South Pacific Division Commander, February 21, 2008, for the Final Integrated Post Authorization Decision Document/ Supplemental Environmental Impact Statement/Environmental Impact Report/Post Authorization Change Report for the San Luis Rey Flood Control Project from College Blvd. to the Pacific Ocean, San Diego, California (SLR PADD/FEIS/FEIR/PAC), July 2007. The proposed action would include active restoration of riparian habitat and floodplain. The proposed site, located along the San Luis Rey River within the existing flood risk management project site, is owned by the City of Oceanside, the project’s non-Federal sponsor, and is herein referred to as the Whelan Mitigation Site.

Scattered tree death contributes to substantial forest loss in California

Nature Portfolio (Springer Nature) | January 20th, 2024

In recent years, large-scale tree mortality events linked to global change have occurred around the world. Current forest monitoring methods are crucial for identifying m

In recent years, large-scale tree mortality events linked to global change have occurred around the world. Current forest monitoring methods are crucial for identifying mortality hotspots, but systematic assessments of isolated or scattered dead trees over large areas are needed to reduce uncertainty on the actual extent of tree mortality. Here, we mapped individual dead trees in California using sub-meter resolution aerial photographs from 2020 and deep learning-based dead tree detection. We identified 91.4 million dead trees over 27.8 million hectares of vegetated areas (16.7-24.7% underestimation bias when compared to field data). Among these, a total of 19.5 million dead trees appeared isolated, and 60% of all dead trees occurred in small groups ( ≤ 3 dead trees within a 30 × 30 m grid), which is largely undetected by other state-level monitoring methods. The widespread mortality of individual trees impacts the carbon budget and sequestration capacity of California forests and can be considered a threat to forest health and a fuel source for future wildfires.