Going with the Flow: How Aquifer Recharge Reduces Flood Risk


Mendonca Dairy property in Crows Landing, California, located next to the San Joaquin River.

With waterways in the San Joaquin Valley more vulnerable to flooding as storms intensify, Flood Managed Aquifer Recharge (Flood-MAR) provides a way to lessen the risk.

On a small scale, aquifers — subsurface natural basins — have benefitted from man-made recharge for decades. Now, a new Department of Water Resources (DWR) assessment shows how Flood Managed Aquifer Recharge, or Flood-MAR, can help reduce flood risk and boost groundwater supplies across large areas of land.

A climate change problem solver, Flood-MAR collects high flow flood waters from heavy precipitation or snow melt and conveys it downstream. There, the flood waters are spread across the land, creating wetland habitat or irrigating fields while also percolating to aquifers underground. The capturing of flood waters during times of peak flows lessens the risk of major flooding during heavy storms. Some of the water later makes its way back to waterways where it can also support ecosystems and riverine habitat. In partnership with the Merced Irrigation District, Sustainable Conservation, and others, DWR experts analyzed how this would work in the Merced River —a 145-mile-long tributary of the San Joaquin River. The Merced River, which flows from the Sierra Nevada to the San Joaquin Valley, could be much more vulnerable to heavy flooding as storms intensify.

With this in mind, and as California’s climate continues to change, the Merced River Flood-MAR Reconnaissance Study tested for a range of different weather conditions and evaluated potential vulnerabilities to climate change in three water resource management areas —water supply, flood, and ecosystems.

"California’s changing climate means more extreme weather – including more frequent droughts and larger, warmer storms that can result in flooding. The Merced study helps demonstrate how Flood-MAR can help mitigate those pressures," said Kamyar Guivetchi, manager of DWR’s Division of Planning. “The study also includes adaptation strategies intended to improve terrestrial and aquatic ecosystems to ensure they are not adversely impacted.”

Benefits of Flood-MAR

To reach their conclusions, the DWR team conducted headwaters to groundwater analysis for 30 climate conditions. The study centered on four steps: how a changing climate will affect floods, surface water, ecosystems, and groundwater; how to convey flood water for recharge; managing reservoirs for recharge based on forecasts or Forecast-Informed Reservoir Operations (FIRO); and the need for new or expanded conveyance infrastructure to help with delivery of flood water to aquifers.

Overall, DWR researchers determined that there was an average of 46,500 acre-feet of water per year available for aquifer recharge based on rainfall amounts over the past century, though that amount could shift as recharge management is modified and the climate continues to change.

The benefits of Flood-MAR are wide-ranging as extreme weather becomes more common. Under Flood-MAR, captured water is spread across the landscape where it creates bird and terrestrial habitat, or supports agricultural activities while recharging depleted aquifers and later flows into adjacent streams or rivers. This recharge process has a positive ripple effect on water supply reliability, flood risk reduction, and drought preparedness. For example, aquifer recharge through Flood-MAR helps offset over-drafting of groundwater, which provides 40% California’s water supply in a typical year (and up to 60 percent in a dry year) while acting as an important buffer against drought, climate change, and land subsidence.  This subsidence can cause the ground to collapse and in recent years parts of the San Joaquin Valley have sunk by about a foot a year

Flood-MAR and the Future

A form of green infrastructure, Flood-MAR also helps California meet its Sustainable Groundwater Management Act goals, which requires local agencies to achieve groundwater sustainability by 2040 or 2042, informs the California Water Plan Update 2023, and advances integrated watershed management planning.

The potential for Flood-MAR in California is vast, particularly in the Central Valley — which has high flood risks and is experiencing severe groundwater depletion and reduced water supplies during the current historic drought. Recharged aquifers can also reduce the risk of natural and human contaminants such as salt from leaching into the soil or degrading water quality. DWR’s Groundwater Water Recharge Assessment Tool can help with recharge planning. However, to realize these benefits, there are challenges to overcome such as negotiating complex water rights — issues outlined in the Flood-MAR Research and Data Development Plan.

The Merced River study informs practitioners and enables researchers to better understand and overcome these challenges to scale-up the implementation of Flood-MAR projects. DWR has received funding to conduct similar watershed studies for the Calaveras River, Stanislaus River, Tuolumne River, the Upper San Joaquin River watersheds.

“With climate change and drought, we are going to need a portfolio of adaptation strategies. Flood-MAR enables us to take advantage of very high flow events for the purpose of recharging depleted aquifers,” said Ajay Goyal, manager of DWR’s Statewide Infrastructure Investigations Branch.

For more information about DWR’s innovative work on recharging aquifers, visit the Flood-MAR website.