Sacramento River

Impacts of the 2014 severe drought on the Microcystis bloom in San Francisco Estuary

Harmful Algae (Elsevier) | February 17th, 2017

The increased frequency and intensity of drought with climate change may cause an increase in the magnitude and toxicity of freshwater cyanobacteria harmful algal blooms

The increased frequency and intensity of drought with climate change may cause an increase in the magnitude and toxicity of freshwater cyanobacteria harmful algal blooms (CHABs), including Microcystis blooms, in San Francisco Estuary, California. As the fourth driest year on record in San Francisco Estuary, the 2014 drought provided an opportunity to directly test the impact of severe drought on cyanobacteria blooms in SFE. A field sampling program was conducted between July and December 2014 to sample a suite of physical, chemical, and biological variables at 10 stations in the freshwater and brackish reaches of the estuary. The 2014 Microcystis bloom had the highest biomass and toxin concentration, earliest initiation, and the longest duration, since the blooms began in 1999. Median chlorophyll a concentration increased by 9 and 12 times over previous dry and wet years, respectively. Total microcystin concentration also exceeded that in previous dry and wet years by a factor of 11 and 65, respectively. Cell abundance determined by quantitative PCR indicated the bloom contained multiple potentially toxic cyanobacteria species, toxic Microcystis and relatively high total cyanobacteria abundance. The bloom was associated with extreme nutrient concentrations, including a 20-year high in soluble reactive phosphorus concentration and low to below detection levels of ammonium. Stable isotope analysis suggested the bloom varied with both inorganic and organic nutrient concentration, and used ammonium as the primary nitrogen source. Water temperature was a primary controlling factor for the bloom and was positively correlated with the increase in both total and toxic Microcystis abundance. In addition, the early initiation and persistence of warm water temperature coincided with the increased intensity and duration of the Microcystis bloom from the usual 3 to 4 months to 8 months. Long residence time was also a primary factor controlling the magnitude and persistence of the bloom, and was created by a 66% to 85% reduction in both the water inflow and diversion of water for agriculture during the summer. We concluded that severe drought conditions can lead to a significant increase in the abundance of Microcystis and other cyanobacteria, as well as their associated toxins.

Implementing Climate-Smart Conservation

Public Policy Institute of California (PPIC) | March 4th, 2025

In our first report, Climate-Smart Tools to Protect California’s Freshwater Biodiversity (Sommer et al. 2024), we reviewed a broad suite of tools available to a

In our first report, Climate-Smart Tools to Protect California’s Freshwater Biodiversity (Sommer et al. 2024), we reviewed a broad suite of tools available to address the urgent problem of safeguarding California’s freshwater biodiversity in the changing climate. This toolbox includes some familiar approaches—such as various ways to improve freshwater habitat—as well as approaches that may be less familiar, more experimental, and more controversial. We also recommended the adoption of a climate-smart conservation planning process, involving a broad range of stakeholders, to prioritize the selection of tools within watersheds and to adaptively implement those tools. In this follow-up report, we explore the feasibility of implementing these tools and climate-smart planning in light of legal, policy, and institutional factors.2 Our analysis draws on an extensive review of the legal literature on ecosystem and protected species management, as well as interviews and small workshops with a wide-ranging set of 45 experts from all over the state. These experts are working on the frontlines of ecosystem policy and management; they include state and federal regulators, members of the environmental conservation community, legal professionals, and representatives of many entities involved in water and land management.

Implementing Ecosystem Based Management

Duke Environmental Law & Policy Forum | June 7th, 2021

Implications of projected climate change for groundwater recharge in the western United States

Journal of Hydrology (Elsevier) | March 1st, 2016

Existing studies on the impacts of climate change on groundwater recharge are either global or basin/location-specific. The global studies lack the specificity to inform

Existing studies on the impacts of climate change on groundwater recharge are either global or basin/location-specific. The global studies lack the specificity to inform decision making, while the local studies do little to clarify potential changes over large regions (major river basins, states, or groups of states), a scale often important in the development of water policy. An analysis of the potential impact of climate change on groundwater recharge across the western United States (west of 100 longitude) is presented synthesizing existing studies and applying current knowledge of recharge processes and amounts. Eight representative aquifers located across the region were evaluated. For each aquifer published recharge budget components were converted into four standard recharge mechanisms: diffuse, focused, irrigation, and mountain-systems recharge. Future changes in individual recharge mechanisms and total recharge were then estimated for each aquifer. Model-based studies of projected climate-change effects on recharge were available and utilized for half of the aquifers. For the remainder, forecasted changes in temperature and precipitation were logically propagated through each recharge mechanism producing qualitative estimates of direction of changes in recharge only (not magnitude). Several key patterns emerge from the analysis. First, the available estimates indicate average declines of 10–20% in total recharge across the southern aquifers, but with a wide range of uncertainty that includes no change. Second, the northern set of aquifers will likely incur little change to slight increases in total recharge. Third, mountain system recharge is expected to decline across much of the region due to decreased snowpack, with that impact lessening with higher elevation and latitude. Factors contributing the greatest uncertainty in the estimates include: (1) limited studies quantitatively coupling climate projections to recharge estimation methods using detailed, process-based numerical models; (2) a generally poor understanding of hydrologic flowpaths and processes in mountain systems; (3) difficulty predicting the response of focused recharge to potential changes in the frequency and intensity of extreme precipitation events; and (4) unconstrained feedbacks between climate, irrigation practices, and recharge in highly developed aquifer systems.

Improving Groundwater Security in the United States

The White House | December 14th, 2024

The U.S. is facing a serious and unprecedented groundwater challenge. In many aquifers, groundwater withdrawal has outpaced natural recharge, which is exacerbated by the

The U.S. is facing a serious and unprecedented groundwater challenge. In many aquifers, groundwater withdrawal has outpaced natural recharge, which is exacerbated by the changing climate and precipitation variability. Much of the water in the major aquifers in the U.S. is fossil water, recharged over 10,000 years ago, and will not be replaced naturally on human timescales. In the western U.S., groundwater resources are being depleted at alarming rates, mostly from agricultural withdrawal. The depletion has caused land subsidence and earth fissures as well as permanent reduction of storage capacity. The depletion has national and global consequences as non-renewable groundwater in the west is embedded in agricultural products transported to the rest of the U. S. and in agricultural commodities exported globally. Many federal agencies have programs to measure the quality and quantity of groundwater, as well as conservation programs for sustainable use of groundwater. PCAST applauds and endorses their efforts as well as those by state governments, non-governmental organizations, professional organizations, local communities, private citizens, and others, to manage their groundwater resources. To ensure the sustainability of this indispensable resource and mitigate risks from its depletion, it is imperative that we enhance our understanding and management of groundwater resources.

Improving Habitats Along Delta Levees: A Review of Past Projects and Recommended Next Steps

Delta Stewardship Council (Delta Council) | January 15th, 2016

This review of habitat improvements along Delta levees was conducted to support the development of the Delta Stewardship Council’s (Council) Delta Levee Investment Stra

This review of habitat improvements along Delta levees was conducted to support the development of the Delta Stewardship Council’s (Council) Delta Levee Investment Strategy (DLIS), which focuses on flood risk reduction as the primary purpose of State levee investments. The report is intended to provide guidance to the Council to ensure that those investments also contribute to long-term improvement of river corridors, with net benefits for fish and wildlife. The Council must ensure that the DLIS helps to implement the Delta Reform Act and the Delta Plan. The Delta Reform Act of 2009 established the Council and defined its mission: to achieve the coequal goals of water supply reliability for California and ecosystem restoration in the Delta, in a manner that protects and enhances the values of the Delta as an evolving place (Water Code section 85054). The Delta Plan includes 14 regulatory policies, including one that calls for levee projects to incorporate habitat benefits, where feasible, and another requiring the use of the best available science and adaptive management. This report is intended to support the application of best available science and adaptive management to habitat improvements along Delta levees. It should be noted that levee-related habitat improvements alone are not expected to provide all the ecosystem benefits needed by native species. These projects take place within the larger context of ecosystem restoration in the Delta and Suisun Marsh, which will require more natural functional flows, restoration and conservation of a wide range of habitat types1, improved water quality, and the management of nonnative invasive species. Nevertheless, given its significant role in Delta levee investments, the State must ensure that these habitat projects are part of a program that provides a net benefit for aquatic species in the Delta.

Improving Infrastructure for Wildlife

Social Science Research Network (SSRN) | February 25th, 2021

In Washington v. United States, 584 U.S. ___ (2018), the Supreme Court required Washington State to improve fish passage through almost 1,000 culverts originally built to

In Washington v. United States, 584 U.S. ___ (2018), the Supreme Court required Washington State to improve fish passage through almost 1,000 culverts originally built to allow streamflow under roads and highways. The case highlighted conflicts between wildlife needs and infrastructure development. Fish passage through outdated or ill-designed culverts is only a small facet of the larger problem of outdated wildlife infrastructure. Impinged migration corridors for ungulates, turtles, and other mobile taxa; levees disconnecting floodplains from rivers; poor water temperature controls on dams; and eroding ecological productivity accompanying aging of reservoirs exemplify the types of challenges to wildlife created by contemporary infrastructure.

In situ allelopathic expression by the invasive amphibious plant, Ludwigia hexapetala (water primrose) across habitat types, seasons, and salinities

Biological Invasions (Springer Link) | August 17th, 2024

Broad infestations of invasive, non-native vegetation have transformed wetlands around the world. Ludwigia hexapetala is a widespread, amphibious invasive plant with a cr

Broad infestations of invasive, non-native vegetation have transformed wetlands around the world. Ludwigia hexapetala is a widespread, amphibious invasive plant with a creeping growth habit in open water and an erect growth habit in terrestrial habitats. In the upper San Francisco Estuary of California, L. hexapetala is increasingly terrestrializing into marshes and this expansion may be facilitated by allelopathy. We conducted the first field-based study on L. hexapetala allelopathy to determine whether (1) three allelochemicals known to be exuded by L. hexapetala are expressed in situ, (2) the allelochemicals are detectable in leaves, soil, and water, and (3) allelopathic expression varies by season, salinity, and growth habit (open water “patch” vs. terrestrial marsh “interface” locations). Water, soil, and L. hexapetala leaves were collected in two freshwater sites and two oligohaline sites in the upper San Francisco Estuary in summer 2021, fall 2021, and spring 2022. Myricitrin and quercitrin, known allelochemicals, and salipurposid, a newly identified polyphenol, were detected in water, soil, and leaves. There were significant differences in allelochemical concentrations under fresh versus oligohaline conditions in water and soil, but not leaves. All three allelochemicals generally had higher concentrations in patch versus interface locations, suggesting that L. hexapetala allelopathy plays a greater competitive role in open water than terrestrial habitats. Leaf concentrations of each allelochemical varied seasonally; however, both myricitrin and salipurposid had heightened concentrations in spring. These results suggest that herbicide application in early spring may be most effective in controlling L. hexapetala terrestrialization from open water to marshes.

Inaction’s Economic Cost for California’s Water Supply Challenges

University of California, Davis (UC Davis) | May 14th, 2025

California’s water system is in for challenges in coming decades as climate, groundwater policy, and environmental regulations reduce availability and increase variabil

California’s water system is in for challenges in coming decades as climate, groundwater policy, and environmental regulations reduce availability and increase variability in water supplies for agricultural and urban uses. A previous report estimated 4 to 9 million acre-feet (maf) per year of unavoidable reductions in existing water supplies, 12% to 25% of today’s water use (Lund et al. 2024). This report estimates the economic costs of not responding to these reductions in water availability.

Incorporating Sea Level Change in Civil Works Programs

U.S. Army Corps of Engineers (USACE) | December 31st, 2013