A Path Forward for California’s Freshwater Ecosystems

Public Policy Institute of California (PPIC) | December 2nd, 2019

Californians rely on freshwater ecosystems for many things: water supply, hydropower, recreation, fisheries, flood risk reduction, biodiversity, and more. These ecosystem

Californians rely on freshwater ecosystems for many things: water supply, hydropower, recreation, fisheries, flood risk reduction, biodiversity, and more. These ecosystems—and the social, economic and environmental benefits they provide—are part of the state’s natural infrastructure. But they are changing in undesirable ways in response to water and land use, pollution, introduction of non-native species, and a changing climate. Declines in native biodiversity are the most direct measure of these changes, with numerous species now protected by state and federal endangered species acts (ESAs) and many times more likely to need protection in future.  For the past 40 years, the ESAs have played a prominent role in managing the state’s freshwater ecosystems. While this approach has prevented extinctions, it also places an emphasis on reducing harm to listed species, rather than improving overall ecosystem condition necessary to recover their populations. And these laws are not forward-looking enough to help species adapt to changing climate and reduce future species listings. This approach also fuels controversy and litigation due to perceptions about trade-offs between species protection and economic uses of land and water.  To maintain the benefits that Californians derive from their freshwater ecosystems—and arrest the decline of native biodiversity—a new approach is needed. We recommend that the state adopt the principles and practices of ecosystem-based management. This involves the simultaneous management of water, land, and organisms to achieve a desired ecosystem condition that benefits both native biodiversity and human well-being. The goal of ecosystem-based planning is to develop a shared vision for the ecosystem, agreement upon a common set of facts, and a unified plan to achieve it. We are not proposing major reforms to state or federal endangered species acts. Rather, we recommend a shift in the way these acts are implemented.  Ecosystem-based management relies on robust governance frameworks that are transparent, collaborative, and supported by science and secure funding. Many programs are starting to adopt its principles and practices, but much more needs to be done. Actions needed to achieve ecosystem-based objectives include setting aside water budgets for the environment and using this water to improve ecosystem condition and create multiple benefits. Binding comprehensive agreements between regulatory agencies, stakeholders, and water users—developed as part of sustainable watershed management plans—should guide implementation. These plans can be used to align agency actions and permitting and can be adopted by the State Water Board as water quality control plans.  California needs to change course in how it manages freshwater ecosystems to protect the many beneficial uses they provide. Ecosystem-based management offers a more comprehensive, flexible, and adaptive approach, and one that is compatible with existing laws. We believe this approach is better able to improve ecosystem outcomes that benefit both people and nature and respond to today’s challenges while preparing for an uncertain future. 

A Review of Delta Fish Population Losses from Pumping Operations in the Sacramento-San Joaquin River Delta

Sacramento Regional County Sanitation District (RegionalSan) | January 30th, 2010

To reduce fish loss at the pumps, the state and federal water export facilities operate facilities which are designed to salvage fish from the water and return them to th

To reduce fish loss at the pumps, the state and federal water export facilities operate facilities which are designed to salvage fish from the water and return them to the Delta. Fish facilities include the SWP Skinner Fish Protection Facility and CVP Tracy Fish Collection Facility. The fish facilities utilize two sets of louvers to prevent fish from entering further into water project operations and ultimately the powerful pumps. The louvers concentrate fish so that they can be removed prior to the water diversions. However, these fish salvage operations are inefficient, as high numbers of fish are lost due to predation in the waterways leading to the fish facilities, and the louvers are inefficient.

A Scientific Assessment of Alternatives for Reducing Water Management Effects on Threatened and Endangered Fishes in California's Bay Delta (2010)

National Academy of Sciences (NAS) | March 19th, 2010

The California Bay-Delta region receives fresh water from the Sacramento and San Joaquin rivers and their tributaries, and some of that water is diverted for agricult

The California Bay-Delta region receives fresh water from the Sacramento and San Joaquin rivers and their tributaries, and some of that water is diverted for agriculture and southern California metropolitan areas. However, the region's growing population and engineered water-control systems have substantially altered the delta ecosystem and have changed the composition of fish species; while some native species have declined, some introduced species have increased. This report provides a scientific evaluation of two "biological opinions" issued by the U.S. Fish and Wildlife Service and the National Marine Fisheries Service in 2008 and 2009, respectively, that require actions to reduce adverse effects of water diversions on delta smelt, Chinook salmon, Central Valley steelhead, and green sturgeon, such as restricting water diversions during certain periods. The report concludes that most of the actions are scientifically justified, but many need clarification concerning details. For example, the Fish and Wildlife Service and the National Marine Fisheries Service actions to reduce risks to delta smelt and juvenile salmon and steelhead by limiting how much water is pumped from the delta in winter have a sound conceptual basis. However, the data do not permit a confident identification of when to limit pumping or the benefits fish receive. Thus careful monitoring, adaptive management, and additional analyses are needed. The report further concludes that our understanding of the risks to the fishes and the benefits likely to accrue from the actions requires an integrated, quantitative analytical framework that ties the various actions together within the species, between smelt and salmonids and sturgeon, and across the watershed. The lack of such an integrated analytic framework hampers both the agencies' and the committee's ability to thoroughly evaluate the effects of the RPAs on the fishes, on water quality and quantity in the delta, and on water operations. Key Messages A proposed U.S. Fish and Wildlife Service action to create or restore 8,000 acres of intertidal and subtidal habitat in the delta is weakly justified, because the relationship between tidal habitats and food availability for smelt is poorly understood. A proposed U.S. Fish and Wildlife Service action to manage the contour line of 2 parts per thousand salinity, called X2, is beneficial to smelt needs further clarification. A proposed U.S. Fish and Wildlife Service action to protect delta smelt by limiting how much water is pumped from the delta to reduce reverse flows in the Old and Middle rivers, two branches of the San Joaquin River is scientifically justified; however, the data do not permit confident identification of when to limit reverse flows or of the benefits fish receive, so careful monitoring, adaptive management, and additional analyses is needed. Adverse effects of all other stressors on the listed fish -- such as contaminants in the delta and structures on rivers that block fishes from access to their spawning habitat -- are potentially large. Regarding a Nation Marine Fisheries Service biological opinion, which applies to the Chinook salmon, steelhead, and green sturgeon in the delta and farther upstream, the committee concluded that on balance the actions are scientifically justified; however, specific environmental triggers, thresholds, and flows should receive additional evaluation that is integrated with the analyses of similar actions for delta smelt. Reversing or even slowing the declines of the listed fish species cannot be accomplished immediately. The effects of an increasing population and the operation of the engineered water-control system have substantially altered the delta ecosystem, including its fish species.

Adaptive Management - Technical Guide

U.S. Department of the Interior (DOI) | January 1st, 2009

The Department of the Interior (DOI) Adaptive Management Working Group (AMWG) sponsored the development of this technical guide to clearly and consistently define adaptiv

The Department of the Interior (DOI) Adaptive Management Working Group (AMWG) sponsored the development of this technical guide to clearly and consistently define adaptive management and describe conditions for its implementation. AMWG membership includes representatives from across DOI’s bureaus and offices. A writing team of resource managers, technical experts, and other specialists worked with AMWG to address four basic questions concerning adaptive management: (1) What is adaptive management? (2) When should it be used? (3) How should it be implemented? (4) How can its success be recognized and measured? These questions were used to organize both the writing effort and the structure of the guide itself, with individual chapters addressing each of the questions. The authors sought to describe adaptive management at an appropriate level of technical detail, while remaining focused on its definition, operational components, and conditions in which it applies. A key challenge was to provide sufficient detail for clarification, while limiting the length and complexity of the document.

Amphibian responses in the aftermath of extreme climate events

Nature Portfolio (Springer Nature) | February 25th, 2020

Climate change-induced extinctions are estimated to eliminate one in six known species by the end of the century. One major factor that will contribute to thes

Climate change-induced extinctions are estimated to eliminate one in six known species by the end of the century. One major factor that will contribute to these extinctions is extreme climatic events. Here, we show the ecological impacts of recent record warm air temperatures and simultaneous peak drought conditions in California. From 2008–2016, the southern populations of a wide-ranging endemic amphibian (the California newt, Taricha torosa) showed a 20% reduction to mean body condition and significant losses to variation in body condition linked with extreme climate deviations. However, body condition in northern populations remained relatively unaffected during this period. Range-wide population estimates of change to body condition under future climate change scenarios within the next 50 years suggest that northern populations will mirror the loss of body condition recently observed in southern populations. This change is predicated on latter 21st century climate deviations that resemble recent conditions in Southern California. Thus, the ecological consequences of climate change have already occurred across the warmer, drier regions of Southern California, and our results suggest that predicted climate vulnerable regions in the more mesic northern range likely will not provide climate refuge for numerous amphibian communities.

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 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.”

Anadromous Salmonid Fish Passage Facility Design

National Marine Fisheries Service (NMFS) | July 26th, 2011

The primary effect of barriers (e.g., hydroelectric dams, water storage projects, irrigation diversions, impassable culverts, etc.) on Pacific salmonids is the reduction

The primary effect of barriers (e.g., hydroelectric dams, water storage projects, irrigation diversions, impassable culverts, etc.) on Pacific salmonids is the reduction in population abundance and productivity through excessive mortality and reduction in habitat quantity and quality. Individuals are lost to the population due to death from passing through turbines, disproportionate predation in reservoirs, entrainment at unscreened or improperly screened diversions, etc. Spatial structure and diversity have also been reduced by the loss of nearly 40% of salmon habitat from dams (NRC 1996), either through complete blockage or inundation. This document is intended to assist with improving conditions for salmonids that must migrate past barriers to complete their life cycle. The task involved in successfully passing fish upstream or downstream of an in-river impediment is a dynamic integration of fish behavior, physiology, and bio-mechanics with hydraulic analysis, hydrologic study, and engineering. Installing a fish passage structure does not constitute providing satisfactory fish passage unless all of the above components are adequately factored into the design. The following document provides criteria, rationale, guidelines, and definitions for the purpose of designing proper fish passage facilities for the safe, timely, and efficient upstream and downstream passage of anadromous salmonids at impediments created by artificial structures, natural barriers (where provision of fish passage is consistent with management objectives), or altered instream hydraulic conditions. This document provides fishway facility design standards for the National Marine Fisheries Service, and is to be used for actions pertaining to the various authorities and jurisdictions of NMFS, including Section 18 of the Federal Power Act (FPA), the Endangered Species Act (ESA), and the Magnuson-Stevens Fishery Conservation and Management Act (MSA) in the Northwest Region (NWR). This document intends to provide generic guidance as an alternative to active participation by NMFS engineers in a design process, for the purpose of providing designs that will be acceptable for fishways that fall within NMFS jurisdictions. If passage facilities are designed and constructed in a manner consistent with these criteria, adverse impacts to anadromous fish migration will be minimized. Instances will occur where a fish passage facility may not be a viable solution for correcting a passage impediment, due to biological, sociological, or economic constraints. In these situations, removal of the impediment or altering operations may be a suitable surrogate for a constructed fish passage facility. In other situations, accomplishing fish passage may not be an objective of NMFS because of factors such as limited habitat or lack of naturally occurring runs of anadromous fish upstream of the site. To determine whether NMFS will use its various authorities to promote or to prescribe fish passage, NMFS will rely on a collaborative approach, considering the views of other fisheries resource agencies, Native American Tribes, non-government organizations, and citizen groups, and will strive to accomplish the objectives in watershed plans for fisheries restoration and enhancement. This document does not address aspects of design other than those that provide for safe and timely fish passage, and to some extent, preservation of aquatic habitat. Structural integrity, public safety, and other aspects of facility design are the responsibility of the principal design engineer, who should ensure that the final facility design meets all other requirements in addition to the fish passage criteria and guidelines contained in this document.

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