Enhancements to EcoAtlas’ CRAM analysis tools: Habitat Development Curves and Ecoregional Cumulative Distribution Function plots (CDFs)

San Francisco Estuary Institute (SFEI) | April 5th, 2016

Enhancing Water Supply through Invasive Plant Removal: A Literature Review of Evapotranspiration Studies on Arundo Donax

Nature Conservancy | February 11th, 2019

Removal of the invasive, non-native plant Arundo donax (Arundo, giant reed) along riparian corridors is being considered by groundwater sustainability agencies

Removal of the invasive, non-native plant Arundo donax (Arundo, giant reed) along riparian corridors is being considered by groundwater sustainability agencies as a potential water savings strategy that could provide co-benefits for groundwater sustainability as well as native ecosystem restoration. Arundo is a fast growing, densely vegetated reed that has purportedly high-water consumption (i.e., transpiration). This paper is intended to help agencies develop estimates of the water supply benefits that could be realized from Arundo removal.

Environmental Characteristics of Select Managed Ponds in the Sacramento–San Joaquin Delta: Implications for Native Fish Conservation and Research

U.S. Geological Survey (USGS) | July 23rd, 2025

The use of wetlands to support native fish research and conservation efforts in the Sacramento–San Joaquin Delta (Delta) of California is a growing priority. The purpos

The use of wetlands to support native fish research and conservation efforts in the Sacramento–San Joaquin Delta (Delta) of California is a growing priority. The purpose of our study was to examine the physiochemical and biological characteristics of select managed ponds in the Delta to determine if they would be suitable habitats for research involving the conservation of delta smelt (Hypomesus transpacificus). We studied 10 managed ponds distributed across the central part of the Delta situated on Bacon Island and Bouldin Island in San Joaquin County, and Holland Tract and Webb Tract islands in Contra Costa County. The managed ponds had a diversity of physical habitat configurations and were not directly connected to waterways surrounding the islands and, therefore, not affected by tides. We studied the managed ponds from approximately November 2021 to December 2023 to assess water quality, zooplankton, fish, and pesticide metrics. Water levels in the managed ponds were managed to varying degrees and were mostly independent of climate-driven wet-dry seasonality. Water quality conditions varied among ponds and were independent of geographic location. Overall, mean monthly chlorophyll a concentration ranged from 15 to 57 (mean=30) micrograms per liter (μg/L), dissolved oxygen concentration ranged from 4 to 9 (mean=7) milligrams per liter (mg/L), pH was 8, salinity was 1 practical salinity units (PSU), specific conductance ranged from 1,202 to 1,839 (mean=1,471) microsiemens per centimeter (μS/cm), and turbidity ranged from 13 to 24 (mean=19) Formazin Nephelometric Units (FNU). Water temperature thresholds that contribute to stress (21 degrees Celsius [°C]) and mortality (28 °C) of delta smelt were often exceeded during summer and fall, though vertical stratification contributed to lower bottom temperatures in the deepest managed ponds, which could potentially provide thermal refugia for delta smelt so long as dissolved oxygen concentrations are suitable. Zooplankton populations were broadly similar among managed ponds and included calanoid and cyclopoid copepods that would be suitable prey for delta smelt. Overall average total zooplankton biomass, as measured with a Schindler-Patalas trap, was 0.6 μg/L (min=0, max=63.6) and peaked during spring at more than 4 μg/L. Fish populations highly varied among the managed ponds with potential predators of delta smelt such as largemouth bass (Micropterus salmoides) and black crappie (Pomoxis nigromaculatus) present in several of the managed ponds; predator distribution among ponds seemed to have been driven primarily by deliberate stocking to facilitate local fisheries. Measured pesticide concentrations were below U.S. Environmental Protection Agency Aquatic Life Benchmarks except for exceedances of three compounds (diuron [herbicide], clothianidin [insecticide], and deltamethrin [pyrethroid insecticide]) in samples collected from ponds on Bouldin Island and Webb Tract. Overall, most managed ponds seemed suitable to support delta smelt, though physical control of potential predators and summer temperature might be needed. The results provide guidance on how to engineer and manage new managed ponds to support research and conservation efforts for delta smelt and other native fishes.

Evaluation of the California State Water Resource Control Board’s Bioassessment Program

California State Water Resources Control Board (SWRCB) | May 15th, 2009

The State of California’s bioassessment, monitoring and assessment (M&A), and water quality standards (WQS) programs were reviewed in January 2008 using the

The State of California’s bioassessment, monitoring and assessment (M&A), and water quality standards (WQS) programs were reviewed in January 2008 using the U.S. EPA’s Critical Technical Elements and Programmatic Review process (Barbour and Yoder 2008; Quasney and Yoder 2008), which evaluates key components of these state programs and existing and planned capacities. The review process results in technical, policy, and management recommendations for building, refining and maintaining functional and effective bioassessment and M&A tools that support the full spectrum of WQS and management programs. This review was conducted by a two-person review team with national expertise at evaluating, building, and implementing state and tribal programs. Bioassessment, the use of resident aquatic biota as direct indicators of the biological integrity of water bodies, is a powerful tool for water resource regulatory programs. The need for state water quality agencies to develop and maintain robust bioassessment programs is underscored by the National Research Council’s critical review of state TMDL, M&A, and WQS programs (National Research Council 2001). The NRC’s review makes clear that all states need better biological endpoints, adequate M&A, and tiered aquatic life uses (TALU) in order to develop and refine appropriate and effective WQS that result in more accurate and appropriate protection for biological resources. While the federal Clean Water Act (CWA) has long required states to protect and restore the chemical, physical, and biological integrity of the nation’s waters, the California Water Boards have only recently begun to develop the tools, expertise and capacity that they will need in order to implement modernized WQS that protect biological integrity. However, because of the substantial investment in the development of bioassessment tools made since the mid-1990s by the state’s Department of Fish and Game, California is now positioned to initiate the process of integrating bioassessments into its WQS and monitoring and assessment programs via the development and implementation of narrative and numeric biocriteria.

Examining the causes and consequences of hybridization during Chinook salmon reintroductions: using the San Joaquin River as a restoration case study of management options

University of California, Davis (UC Davis) | June 15th, 2014

Successful salmonid restoration efforts depend upon an understanding of the evolutionary processes that historically shaped population diversity, as well as the realities

Successful salmonid restoration efforts depend upon an understanding of the evolutionary processes that historically shaped population diversity, as well as the realities of currently available, altered river systems. Habitat alterations over the past century have dramatically changed the ecological forces that shaped salmonid speciation and evolution, bringing formerly separate and distinct populations into contact and in some cases leading to hybridization. Hybridization can threaten the genetic diversity within salmonid species and may affect the outcomes of restoration efforts. Here we use the San Joaquin River Restoration as a case study to discuss some of the genetic challenges of Chinook salmon restoration in a newly reopened habitat. We discuss a range of genetic management strategies—from passive reintroduction to tightly managed, active reintroduction—and the strengths and weaknesses of each approach.

Factors Affecting Marsh Vegetation at the Liberty Island Conservation Bank in the Cache Slough Region of the Sacramento–San Joaquin Delta, California

U.S. Geological Survey (USGS) | July 5th, 2017

The Liberty Island Conservation Bank (LICB) is a tidal freshwater marsh restored for the purpose of mitigating adverse effects on sensitive fish populations elsewhere in

The Liberty Island Conservation Bank (LICB) is a tidal freshwater marsh restored for the purpose of mitigating adverse effects on sensitive fish populations elsewhere in the region. The LICB was completed in 2012 and is in the northern Cache Slough region of the Sacramento–San Joaquin Delta. The wetland vegetation at the LICB is stunted and yellow-green in color (chlorotic) compared to nearby wetlands. A study was done to investigate three potential causes of the stunted and chlorotic vegetation: (1) improper grading of the marsh plain, (2) pesticide contamination from agricultural and urban inputs upstream from the site, (3) nitrogen-deficient soil, or some combination of these. Water samples were collected from channels at five sites, and soil samples were collected from four wetlands, including the LICB, during the summer of 2015. Real-time kinematic global positioning system (RTK-GPS) elevation surveys were completed at the LICB and north Little Holland Tract, a closely situated natural marsh that has similar hydrodynamics as the LICB, but contains healthy marsh vegetation. The results showed no significant differences in carbon or nitrogen content in the surface soils or in pesticides in water among the sites. The elevation survey indicated that the mean elevation of the LICB was about 26 centimeters higher than that of the north Little Holland Tract marsh. Because marsh plain elevation largely determines the hydroperiod of a marsh, these results indicated that the LICB has a hydroperiod that differs from that of neighboring north Little Holland Tract marsh. This difference in hydroperiod contributed to the lower stature and decreased vigor of wetland vegetation at the LICB. Although the LICB cannot be regraded without great expense, it could be possible to reduce the sharp angle of the marsh edge to facilitate deeper and more frequent tidal flooding along the marsh periphery. Establishing optimal elevations for restored wetlands is necessary for obtaining the full suite of ecosystem services provided by tidal wetlands. A better system of tidal benchmarks throughout the delta is needed to help restoration practitioners correctly grade the elevation of newly restored wetlands.

Feather River Salmonid Habitat Improvement Project Proposed Mitigated Negative Declaration

California Department of Water Resources (DWR) | October 6th, 2022

An initial study/proposed mitigated negative declaration (IS/MND) has been prepared to assess the proposed project’s potential effects on the physical environment and t

An initial study/proposed mitigated negative declaration (IS/MND) has been prepared to assess the proposed project’s potential effects on the physical environment and the significance of those effects. Based on the analysis conducted in the IS, DWR has determined that the proposed project would not have any significant adverse effects on the environment because environmental commitments and mitigation measures would be implemented to reduce impacts to a less-than-significant level.

Fill Mead First: A Technical Assessement

Utah State University | October 11th, 2016

The Fill Mead First (FMF) plan would establish Lake Mead reservoir as the primary water storage facility of the main-stem Colorado River and would relegate Lake Powell re

The Fill Mead First (FMF) plan would establish Lake Mead reservoir as the primary water storage facility of the main-stem Colorado River and would relegate Lake Powell reservoir to a secondary water storage facility to be used only when Lake Mead is full. The objectives of the FMF plan are to re-expose some of Glen Canyon’s sandstone walls that are now inundated, begin the process of re-creating a riverine ecosystem in Glen Canyon, restore a more natural stream-flow, temperature, and sediment-supply regime of the Colorado River in the Grand Canyon ecosystem, and reduce system-wide water losses caused by evaporation and movement of reservoir water into ground-water storage. 

Final Report on the recovery of the Upper Sacramento River - subsequent to the 1991 Cantara spill

Cantara Trustee Council | June 18th, 2007

The Cantara Trustee Council (CTC), and the Cantara Program, operated for a period of 12 years, from 1995-2007. During that time, the CTC funded numerous projects which in

The Cantara Trustee Council (CTC), and the Cantara Program, operated for a period of 12 years, from 1995-2007. During that time, the CTC funded numerous projects which included restoration activities, land acquisition and protection, research, and public education. The purpose of this document is to leave a summary record of events that occurred due to the 1991 Cantara spill. It is our intent to provide a condensed presentation of the spill event, the legal processes following the spill, including the formation of the CTC, the formation of the Cantara Program, and the development of guiding plans and documents used by the CTC in the disbursement of settlement funds.

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.