Satellite imagery from NOAA's GOES system taken during California's historic 2023 water year showing the Sierra Nevada with colored overlays delineating the five study areas of the San Joaquin Basin Flood MAR Watershed Studies (from north to south: Calaveras, Stanislaus, Tuolumne, Merced, and Upper San Joaquin)

Capturing floodwaters and coordinated water management are key to replenishing groundwater, supporting ecosystems and strengthening climate resilience across the San Joaquin Basin

December 3, 2025 - SACRAMENTO, Calif. – California’s San Joaquin Basin is at the center of the state’s water challenges, with decades of groundwater overdraft and increasingly severe floods putting water supplies, communities, agriculture, and the environment at risk. The Department of Water Resources’ (DWR) newly released San Joaquin Basin Flood-MAR Watershed Studies assess how climate change is intensifying these water management challenges across the Calaveras, Stanislaus, Tuolumne, Merced, and Upper San Joaquin watersheds and identifies strategies to help the San Joaquin Valley prepare and adapt to a more variable future.

“San Joaquin Valley communities will be dramatically shaped by growing extremes in drought and flood, and our capacity to respond to them. The Watershed Studies begin a broad path forward for the Valley – outlining the risk if we do nothing and what we can gain if we begin acting together now,” said DWR Director Karla Nemeth. “They show how coordinated watershed investments can protect our water supplies and support agriculture and ecosystems, reduce flood risk and provide our partners the information they need to protect communities.”

Turning Floods into a Resource

The Watershed Studies explore how capturing and storing floodwater underground – a practice known as Flood-Managed Aquifer Recharge (Flood-MAR) – can turn extreme events into opportunities.

The Watershed Studies investigated a comprehensive strategy combining forecast-informed reservoir operations (FIRO) with managed aquifer recharge (MAR). FIRO-MAR uses improved weather forecasting to guide how reservoirs store and release water thanks to technology that has advanced substantially over the past 20 years developed in partnership with Center for Western Weather and Water Extremes and others. Operators can use FIRO to create storage opportunities in multiple ways. When storms are forecast, they can release water preemptively to open more space to absorb incoming flood flows, timing releases to allow communities to store that water underground. During non-storm periods, operators can strategically hold and release water to recharge groundwater or support other water supply goals, expanding storage opportunities beyond traditional flood management operations.

Utilizing FIRO-MAR has the potential to increase the volume of recharge more than fourfold, and it can greatly diminish the size and frequency of flood flows. The reoperation of reservoirs in the comprehensive strategy also enhances habitat by creating temporary, seasonal wetlands for shorebirds and improving instream flows for fish.

The Path Forward

These studies are meant to show water managers, decision-makers, and investors how potential reservoir operational changes can be used to optimize basin-wide flood risk management, water supply, and ecosystem benefits. Water rights remain a primary consideration for implementing recharge projects. To implement the studies’ recommendations, tradeoffs must be examined, and new agreements would be needed with existing water right holders and other partners. The Watershed Studies did not attempt to fully neutralize negative impacts.

The Watershed Studies open the door for pilot projects that could be implemented to learn from real-world experience and improve over time. Implementing FIRO-MAR across the San Joaquin Basin would require expanded recharge operations, improvements to local conveyance systems, and enhancements to instream flow management. The Watershed Studies assessment of FIRO provides a planning-level illustration of FIRO-MAR’s potential but does not fully determine the feasibility of strategies. The owner of each reservoir will need to determine the applicability of the strategies and necessary water right actions before any final plan or new operation can be put into practice. Those determinations would be made in partnership with local, state, and federal agencies.

While the Watershed Studies create a path forward throughout the region, leaders within DWR recognize that the studies will benefit critical work being done across the department.

“The San Joaquin Basin Watershed Studies provide new insights that will help inform the State’s long-term flood management strategy. By integrating watershed-scale actions into future updates to the Central Valley Flood Protection Plan, California can better protect people from flooding and deliver broader water management benefits across the San Joaquin Basin.” –

Laura Hollender, Deputy Director for Flood Management & Dam Safety

“Many groundwater basins are facing enormous challenges to end overdraft and achieve groundwater sustainability especially with growing weather extremes. The San Joaquin Valley Watershed Study provides cutting edge scientific analysis that identifies opportunities that could greatly replenish groundwater basins.” – Paul Gosselin, Deputy Director of Sustainable Water Management

“Over the past 20 years we've made significant progress in reconnecting fish to floodplains and historic habitats. The next phase of ecosystem recovery calls for us to make smarter decisions about when we move water through the valley and our delta to maximize the ecological return on investments in landscape restoration.” – James Newcomb, Deputy Director for Habitat Restoration

“Understanding the connection between groundwater pumping, managed aquifer recharge, and operations of the State Water Project is essential for managing water resources in a way that’s transparent, resilient and sustainable. These watershed studies are a major leap forward in doing so.” – John Yarbrough, Deputy Director of the State Water Project.

Studies and Additional Resources

The San Joaquin Basin Flood-MAR Watershed Studies include a summary document and five individual reports that together provide an in-depth look at the future climate challenges and adaptation opportunities.

• Basinwide Summary and Next Steps
• Calaveras Watershed Study Area Report
• Stanislaus Watershed Study Area Report
• Tuolumne Watershed Study Report
• Merced Watershed Study Report
• Upper San Joaquin Watershed Study Report

Find answers to frequently asked questions about the Watershed Studies or explore fact sheets for each watershed, additional resources, data, and information about the Watershed Studies at www.water.ca.gov/watershedstudies.

Source: CA. DWR