San Joaquin River

Impact of extreme drought and incentive programs on flooded agriculture and wetlands in California’s Central Valley

PeerJ | June 29th, 2018

Between 2013 and 2015, a large part of the western United States, including the Central Valley of California, sustained an extreme drought. The Central Valley is recogniz

Between 2013 and 2015, a large part of the western United States, including the Central Valley of California, sustained an extreme drought. The Central Valley is recognized as a region of hemispheric importance for waterbirds, which use flooded agriculture and wetlands as habitat. Thus, the impact of drought on the distribution of surface water needed to be assessed to understand the effects on waterbird habitat availability.Methods: We used remote sensing data to quantify the impact of the recent extreme drought on the timing and extent of waterbird habitat during the non-breeding season (July–May) by examining open water in agriculture (rice, corn, and other crops) and managed wetlands across the Central Valley. We assessed the influence of habitat incentive programs, particularly The Nature Conservancy’s BirdReturns and The Natural Resources Conservation Service’s Waterbird Habitat Enhancement Program (WHEP), at offsetting habitat loss related to drought.Results: Overall, we found statistically significant declines in open water in post-harvest agriculture (45–80% declines) and in managed wetlands (39–60% declines) during the 2013–2015 drought compared to non-drought years during the period of 2000–2011. Crops associated with the San Joaquin Basin, specifically corn, as well as wetlands in that part of the Central Valley exhibited larger reductions in open water than rice and wetlands in the Sacramento Valley. Semi-permanent wetlands on protected lands had significantly lower (39–49%) open water in the drought years than those on non-protected lands while seasonal wetlands on protected lands had higher amounts of open water. A large fraction of the daily open water in rice during certain times of the year, particularly in the fall for BirdReturns (61%) and the winter for WHEP (100%), may have been provided through incentive programs which underscores the contribution of these programs. However, further assessment is needed to know how much the incentive programs directly offset the impact of drought in post-harvest rice by influencing water management or simply supplemented funding for activities that might have been done regardless. Discussion: Our landscape analysis documents the significant impacts of the recent extreme drought on freshwater wetland habitats in the Central Valley, the benefits of incentive programs, and the value of using satellite data to track surface water and waterbird habitats. More research is needed to understand subsequent impacts on the freshwater dependent species that rely on these systems and how incentive programs can most strategically support vulnerable species during future extreme drought.

Impacts of California’s Five-Year (2012-2016) Drought on Hydroelectricity Generation

Pacific Institute | April 13th, 2017

The severe hydrological drought afflicting California between 2012 and 2016 has ended, with an extremely wet winter beginning in October 2016. That five-year per

The severe hydrological drought afflicting California between 2012 and 2016 has ended, with an extremely wet winter beginning in October 2016. That five-year period was the driest and hottest in the instrumental record going back to the late 1800s. Impacts on communities, ecosystems, farmers, and the economy were widespread but have been unevenly distributed. The Pacific Institute has regularly analyzed the consequences of California droughts, beginning with comprehensive assessments of the 1987-1992 drought (Gleick and Nash 1991, Nash 1993), the 2007-2009 drought (Christian-Smith et al. 2011), and this most recent drought (Cooley et al. 2015, Gleick 2015, Cooley et al. 2016, Feinstein et al. 2017). This analysis is the third assessment of the impacts of the drought on hydropower production and greenhouse gas emissions from California’s energy sector (Gleick 2015, Gleick 2016). This analysis finds that during the five years ending September 30, 2016 (the end of the 2016 “water year”), hydropower generation was substantially below average, and the associated economic cost to California ratepayers was approximately $2.45 billion dollars. The additional combustion of fossil fuels for electricity generation also led to a 10 percent increase in carbon dioxide emissions from California’s in-state power plants (CARB 2015) along with increased emissions of other pollutants.

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.

Impacts of the California Drought from 2007 to 2009: Surprising Outcomes for California’s Agriculture, Energy, and Environment

Pacific Institute | June 16th, 2011

California’s three-year drought, which ended with this season’s cool and wet weather, had complicated and serious impacts that have been poorly understood and reporte

California’s three-year drought, which ended with this season’s cool and wet weather, had complicated and serious impacts that have been poorly understood and reported. Some of the impacts were expected; others were surprising. The Pacific Institute has just completed a nine-month assessment of new data from California’s agricultural, energy, and environmental sectors to evaluate actual consequences of the drought for the state. Analysis of state and federal data released over the past year finds that contrary to much of the media reporting, California’s agricultural community proved flexible and resilient, generating agri­cultural revenues in 2007, 2008, and 2009 that were the highest on record. And agriculture-related occupations remained a stable portion of total jobs available in areas directly impacted by water supply restrictions. Less frequently reported were the substantial impacts on energy production and aquatic ecosystems during the drought, which were economically and environmentally significant. “More severe drought is inevitable, and the U.S. – and California in particular – has not reformed drought monitoring, evaluation, planning, and response strategies the way other countries and regions have,” said Juliet Christian-Smith, senior research associate at the Pacific Institute and lead author of the report. “To become more resilient to future droughts, it will be critical to shift from crisis-driven responses to long-term mitigation strategies.” The Pacific Institute analysis, Impacts of the California Drought from 2007-2009, focused on three drought-sensitive sectors: agricultural production, energy production, and ecosystem health.  

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.