Final EPA-USGS Technical Report: Protecting Aquatic Life from Effects of Hydrologic Alteration

U.S. Geological Survey (USGS) | December 6th, 2016

The natural flow regime of a water body, defined as its characteristic pattern of flow magnitude, timing, duration, frequency, and rate of change, plays a critical role i

The natural flow regime of a water body, defined as its characteristic pattern of flow magnitude, timing, duration, frequency, and rate of change, plays a critical role in supporting the chemical, physical, and biological integrity of streams and rivers and the services they provide. Human-induced alteration of the natural flow regime can degrade a stream’s physical and chemical properties, leading to loss of aquatic life and reduced aquatic biodiversity. Protecting aquatic life from the effects of flow alteration involves maintaining multiple components of the flow regime within their typical range of variation. This report was developed (1) to serve as a source of information for states, Tribes, and territories on the natural flow regime and potential effects of flow alteration on aquatic life and (2) to provide a flexible, nonprescriptive framework that can be used to quantify targets for flow regime components that are protective of aquatic life. As a supplementary resource, Appendix A was added to provide examples where states and Tribes have applied Clean Water Act (CWA) tools to protect aquatic life from altered flow. Anthropogenic landscape change and water management activities are modifying flood flows, base flows, peak-flow timing, and other flow characteristics in streams and rivers throughout the United States. Under natural conditions, a stream’s flow regime is determined by hydrologic properties at two scales, the upstream drainage area (catchment) and the local, reach scale. At the catchment scale, climate determines patterns of water and energy input over time, whereas physical characteristics like soils, geology, and topography determine pathways, rates of runoff, and routing through the stream network. Reach-scale factors such as local groundwater dynamics further influence natural flow regime characteristics. Human activities that alter the natural flow regime also occur at both the catchment and reach scales and include impoundments, channelization, diversions, groundwater pumping, wastewater discharges, urban development, thermoelectric power generation, and agricultural practices. Many of these activities alter hydrologic processes like infiltration, groundwater recharge, channel storage, or routing and lead to flow conditions outside the natural range of variation. Others directly add or remove water from a stream such that flows are uncommonly high or low over long periods of time. Occurring in conjunction with these activities is climate change. Climate trends observed in recent decades and future projections (for example, rising ambient air temperatures, increasing frequency of heavy precipitation events, reductions in the thickness of snow pack and ice) may magnify the effects of other anthropogenic processes on the natural flow regime. Alteration of the natural flow regime can have cascading effects on the physical, chemical, and biological properties of riverine ecosystems. Effects on physical properties include altered channel geomorphology (channel incision, widening, bed armoring, etc.), reduced (or augmented) riparian and flood-plain connectivity, and reduced (or augmented) longitudinal (upstream-downstream) and vertical (surface water/groundwater) connectivity. Effects on water quality can also result from altered flow magnitudes. For example, salinity, sedimentation, and water temperature can increase when flow volumes are reduced, whereas erosion and sediment transport can increase with amplified flow volumes. These changes to a stream can in turn lead to the degradation of aquatic life as a result of the loss and disconnection of high-quality habitat. Furthermore, altered flows can fail to provide the cues needed for aquatic species to complete their life cycles and can encourage the invasion and establishment of non-native aquatic species. The ability of a water body to support aquatic life is tied to the maintenance of key flow-regime components. Efforts to implement strategies to protect aquatic life from flow alteration will be most effective if numeric targets are identified for flow-regime components that equate to intact and healthy aquatic communities. This report presents a flexible framework that can be used to quantify flow targets that incorporate U.S. Environmental Protection Agency Guidelines for Ecological Risk Assessment (ERA) and concepts from contemporary environmental flow literature. The framework consists of eight steps that begin with identifying biological goals and assessment endpoints and end with an evaluation of effects on aquatic life under varying degrees of flow alteration. The framework does not prescribe any particular analytical approach (for example, statistical or mechanistic modeling methodology), but rather focuses on the process and information needed to evaluate relations between flow and aquatic life and the development of narrative or numeric flow targets.

Final land management plan for the Yolo Bypass Wildlife Area

California Department of Fish and Wildlife (CDFW) | June 9th, 2008

The Yolo Bypass Wildlife Area (Wildlife Area) comprises approximately 16,770 acres of managed wildlife habitat and agricultural land within the Yolo Bypass (Bypass). The

The Yolo Bypass Wildlife Area (Wildlife Area) comprises approximately 16,770 acres of managed wildlife habitat and agricultural land within the Yolo Bypass (Bypass). The Bypass conveys seasonal high flows from the Sacramento River to help control river stage and protect the cities of Sacramento, West Sacramento, and Davis and other local communities, farms, and lands from flooding. Substantial environmental, social and economic benefits are provided by the Yolo Bypass, benefiting the people of the State of California. The California Department of Fish and Game (DFG), as part of the Resources Agency of the State of California, has the following mission to guide its planning and operations: “The mission of the Department of Fish and Game is to manage California’s diverse fish, wildlife, and plant resources, and the habitats upon which they depend, for their ecological values and for their use and enjoyment by the public.” The stated purpose of the Yolo Bypass Wildlife Area Land Management Plan (LMP) is to: guide management of habitats, species, appropriate public uses, and programs to achieve DFG’s mission; direct an ecosystem approach to managing the Yolo Bypass Wildlife Area in coordination with the objectives of the CALFED Ecosystem Restoration Program (ERP); identify and guide appropriate, compatible public-use opportunities within the Yolo Bypass Wildlife Area; direct the management of the Yolo Bypass Wildlife Area in a manner that promotes cooperative relationships with adjoining private-property owners; establish a descriptive inventory of the sites and the wildlife and plant resources that occur in the Yolo Bypass Wildlife Area; provide an overview of the Yolo Bypass Wildlife Area’s operation, maintenance, and personnel requirements to implement management goals, and serve as a planning aid for preparation of the annual budget for the Bay-Delta Region (Region 3); and present the environmental documentation necessary for compliance with state and federal statutes and regulations, provide a description of potential and actual environmental impacts that may occur during plan management, and identify mitigation measures to avoid or lessen these impacts. This LMP was prepared through a partnership between DFG and the Yolo Basin Foundation (Foundation) and with the benefit of an extensive public-input program. DFG provided overall guidance to the planning process and was responsible for all decisions regarding the content of the LMP. The Foundation was responsible for coordinating substantial stakeholder outreach and facilitating stakeholder input in the LMP development. The Foundation was instrumental in the development of environmental education and interpretation programs at the Yolo Bypass Wildlife Area and helped facilitate the documentation of these programs in this plan. The public-outreach program featured six focus group meetings conducted before initiation of LMP development (2002); a total of 37 Yolo Bypass Working Group Meetings (1999 to 2006; updates on developments at the Yolo Bypass Wildlife Area have been a frequent topic of discussion); one advertised public meeting for initial input (December 12, 2005, in Davis, attended by 30 persons); five additional focus group meetings to receive input on the Preliminary Draft LMP (March and April, 2006), one advertised public meeting for input on the Draft LMP and Initial Study. Appendix A provides a summary of the comments received at the public meetings and examples of the various communication devices that were used to publicize the planning process.

Final Regulatory Flexibility Analysis for the Final Rule Defining "Harm" in the Definition of "Take" in the ESA

National Marine Fisheries Service (NMFS) | October 1st, 1999

The National Marine Fisheries Service (NMFS) is issuing a final rule defining the term "harm" contained in the definition of "take" under the Endangered Species Act of 19

The National Marine Fisheries Service (NMFS) is issuing a final rule defining the term "harm" contained in the definition of "take" under the Endangered Species Act of 1973 (ESA). This rulemaking will codify NMFS' interpretation of "harm" is that habitat modification can result in a take under the ESA. The Regulatory Flexibility Act (RFA), 5 U.S.C. 601 et seq. requires the preparation of an initial and final Regulatory Flexibility Analyses unless an agency determines that a rule, if promulgated, will not have a significant economic impact on a substantial number of small entities. In the May 1, 1998 Federal Register Notice for the proposed rule to define harm (63 FR 24148-24150), NMFS opined that the proposed rule, if adopted, would not have a significant economic impact on a substantial number of small entities, as described in the Regulatory Flexibility Act, and that therefore, a Regulatory Flexibility Analysis would not be required for adoption of the final rule. However, numerous public comments were received in response to the Federal Register Notice and accompanying draft EA requesting that a Regulatory Flexibility Analysis be performed. This document constitutes NMFS' Final Regulatory Flexibility Analysis.

Final Value Planning Study Report for Through Delta Facility, Sacramento, California

California Department of Water Resources (DWR) | July 1st, 2007

Financing Delta Improvements and Environmental Mitigation

California Research Bureau (CRB) | September 1st, 2008

Resolution of the Delta’s water supply, water quality, and fish problems may involve building various structures, possibly including gates, pumps, canals, levees, and d

Resolution of the Delta’s water supply, water quality, and fish problems may involve building various structures, possibly including gates, pumps, canals, levees, and dams, and undertaking landscaping rearrangements to improve habitat for several species of flora and fauna. Resolution also involves changing water flow regimes in ways that would make more or less water, but probably less, available for human uses. This work and these changes will cost serious money. Cost estimates for many of these actions have not yet been developed. This paper explores approaches to financing these “improvements” and “mitigations.” While a little abstract, this is abstraction that matters. It will determine from whose pockets a good deal of money will come. California has a long history of financing water projects. The first section of this paper reviews this history, in hopes of identifying water-financing principles that might be adapted to Delta improvements and mitigation. Some deep-seated controversies about how Delta improvements should be financed have roots in this history, and it may be helpful to point them out. A core idea in California’s approach to financing water projects is that beneficiaries should pay for them. Decades ago, this was a straightforward proposition – people or water districts should pay for the necessary dams, canals, and pumps and the costs of operating them in proportion to the amount of water they received. In the current age of rising environmental sensitivity, it is a little muddier. An alternative formulation that applies, at least crudely, to housing developments and highway projects, is that project proponents should pay to mitigate at least some of the environmental harm that their project is likely to cause. The second section of this paper explores this controversial subject. It seems unlikely that any consensus can be reached about how to finance facilities in the Delta without reaching some agreement about how to deal with this matter. This paper was first issued in July, 2008. This version contains a few clarifications made in response to the Blue Ribbon Task Force’s reviewers. The author is grateful for their suggestions.

Fish & Wildlife Groundwater Planning Considerations

California Department of Fish and Wildlife (CDFW) | June 6th, 2019

In 2014, California passed the Sustainable Groundwater Management Act (SGMA) (AB1739, SB 1168, SB 1319), authorizing local groundwater sustainability agencies (GSAs) to d

In 2014, California passed the Sustainable Groundwater Management Act (SGMA) (AB1739, SB 1168, SB 1319), authorizing local groundwater sustainability agencies (GSAs) to develop groundwater sustainability plans (GSPs) for a subset of California’s alluvial aquifers. To comply with SGMA, GSAs must achieve sustainable groundwater management, defined by SGMA as the avoidance of locally-defined undesirable results. To achieve sustainability, GSAs must develop and implement effective groundwater management plans that consider the interests of all beneficial uses and users of groundwater, including environmental users of groundwater. [Water Code § 10723.2.] In many groundwater basins, fish and wildlife that rely on groundwater are among these beneficial uses and users. Many sensitive species and habitats comprise groundwater dependent ecosystems (GDEs), which are natural communities that rely on groundwater to sustain all or a portion of their water needs. The unsustainable use of groundwater can impact the shallow aquifers and interconnected surface waters on which GDEs depend and may lead to adverse impacts on fish and wildlife. As trustee for California’s fish and wildlife resources, CDFW intends to engage as a stakeholder in groundwater planning processes (where resources are available) to represent the groundwater needs of GDEs and fish and wildlife beneficial uses and users of groundwater. The information provided here is intended to help local groundwater planners, groundwater planning proponents and consultants, and CDFW staff work together to consider the needs of fish and wildlife when developing groundwater management plans and implementing SGMA. The document includes three categories of groundwater planning considerations: Scientific Considerations Management Considerations; and Legal, Regulatory, and Policy Considerations. Links to additional guidance and considerations developed by CDFW and other organizations that address the impacts of groundwater pumping on GDEs and depletion of interconnected surface water can be found at the end of this document. Except to the extent that this document directly references existing statutory or regulatory requirements, use of these groundwater planning considerations is not mandated under law and should not be interpreted as a rule, regulation, order, or standard for local groundwater plans. Practical application of these considerations must be based on the best available information and groundwater basin-specific conditions.

Fish & Wildlife Groundwater Planning Considerations: Freshwater Wetlands

California Department of Fish and Wildlife (CDFW) | June 6th, 2019

 In 2014, California passed the Sustainable Groundwater Management Act (SGMA) (AB1739, SB 1168, SB 1319), authorizing local groundwater sustainability agencies to develo

 In 2014, California passed the Sustainable Groundwater Management Act (SGMA) (AB1739, SB 1168, SB 1319), authorizing local groundwater sustainability agencies to develop groundwater sustainably plans for a subset of California’s alluvial aquifers. This document provides considerations to assist local groundwater sustainability agencies in avoiding or minimizing adverse impacts to freshwater wetland beneficial uses and users of groundwater in local groundwater management planning and implementation. The information provided is intended to help local groundwater planners, groundwater planning proponents and consultants, and California Department of Fish and Wildlife (CDFW) staff work together to protect wetlands as a public trust resource. 

Fish and Game Commission Twenty-Second Biennial Report for the Years 1910-1912

State of California | December 31st, 1912

Fish Bulletin 133. Ecological Studies of The Sacramento-San Joaquin Estuary Part 1: Zooplankton, Zoobenthos, and Fishes of San Pablo and Suisun Bays, Zooplankton and Zoobenthos of the Delta

California Department of Fish and Wildlife (CDFW) | September 9th, 1965

The Sacramento and San Joaquin Rivers have a common estuary. These two streams meet in the center of California's central valley to form the Delta (Figure 1). A hundred y

The Sacramento and San Joaquin Rivers have a common estuary. These two streams meet in the center of California's central valley to form the Delta (Figure 1). A hundred years ago the Delta was an extensive tidal marsh, but it has been almost entirely reclaimed for agriculture. The Delta now includes about 738,000 acres of land and water, 700 miles of navigable channels, and 30 large, below sea level islands. About 39,000 acres are covered by water. Some Delta channels are edged with narrow stretches of intertidal marsh but most of them have steep banks of mud or are covered with large cobbles to prevent erosion. They vary in width from a few hundred feet to a mile and are seldom more than 30 to 40 feet deep. In some areas there are small "waste" islands that flood during high tides. These waste islands and levees that surround all Delta channels are covered with an assortment of emergent aquatic plants, grasses, forbs, shrubs, and trees. Water heading toward the sea from the Delta passes through Suisun Bay, which is merely the wide combination of the Sacramento and San Joaquin Rivers below the Delta. Thirty-six percent of Suisun Bay is flooded by less than 3 feet of water at mean lower-low tide, and at this stage about 3,000 acres of intertidal zone is exposed. Richard Painter (see p. 40) has included a map of the 6-foot contour. From Suisun Bay the water flows through the 6-mile long and up to 100 feet deep Carquinez Strait into San Pablo Bay. Almost 60 percent of San Pablo Bay's 73,000 acres is less than 6 feet deep at mean lower-low tide. San Pablo Bay has a much more extensive intertidal area than Suisun Bay. San Pablo Bay water flows into San Francisco Bay and then through the narrow Golden Gate into the Pacific Ocean. The investigations reported on in this bulletin were geographically limited to the upper and middle portions of the estuary—from the Delta through San Pablo Bay. We have not investigated below San Pablo Bay. McCarty et al (1962) described south San Francisco Bay, and Storrs, Selleck, and Pearson (1964) described north San Francisco Bay. Gillian (1957) wrote an interesting and useful popular account of the entire bay.

Fish Collections and Secondary Louver Efficiency at the Tracy Fish Collection Facility: October 1993 to September 1995

U.S. Bureau of Reclamation (USBR) | May 29th, 1998