A little-publicized but curious part of the emergency drought legislation signed by Gov. Jerry Brown in March advances hundreds of millions of dollars to shore up and replace aging levees in flood-prone areas of the state.

Drought relief through better flood control? Really?

As it turns out, some flood protection projects are important during droughts. Strategically removing sections of old levees or rebuilding them hundreds or thousands of feet from their original riverbank sites can significantly replenish aquifers during wet years, providing badly needed supplies during droughts.

The drought relief package accelerates the appropriation of $660 million from a 2006 flood protection bond act (Proposition 1E) that specifically authorizes construction of so-called “setback levees” because of the groundwater recharge and other benefits they provide.

Setback levees are not new. The Dutch have them to improve flood control; allowing floodwaters to spill onto undeveloped or farmed floodplains lowers the flood risk for communities downstream. Their use in California, however, has been much more limited. Local flood control and reclamation districts have focused more on keeping century-old levees intact.

Some agencies are beginning to rethink this approach, as growing numbers of studies point to the multiple economic and environmental benefits of reconnecting rivers with their floodplains — long separated by levees.

It’s easy to forget that the Central Valley was once a vast wetland. Before we built dams and straightjacketed rivers with levees, storms would swell rivers out of their normal banks and onto floodplains. The water would percolate into the ground and refill aquifers. Those inundated floodplains also served as nurseries for fish, with abundant insect food and ideal water temperatures for growing bigger and faster — improving their odds of survival in the ocean.

Today, with only 5 percent of the floodplains left undeveloped in California, there are few opportunities for floods to refill aquifers. The levees built in the late 1800s and early 1900s to protect cities and farms from flooding now act as barriers to residents and farmers needing to expand groundwater supplies for drinking water and irrigation.

Three years ago our team of watershed scientists set up an experiment on the Cosumnes River Preserve near Lodi to better understand the relationship of river levees to groundwater recharge. The Nature Conservancy removed about 750 feet of old riverside levee and breached additional levees to allow floods more access onto the floodplain. Scientists monitored the biophysical response.

Preliminary results have been encouraging. Removing the levee on the Nature Conservancy’s 500-acre experimental floodplain appreciably replenished local aquifers and reduced flood risks for area landowners. Just a brief storm in early February added roughly 100 to 300 acre-feet of water to local groundwater stores.

Now that this floodplain will become inundated more frequently, the recharge will continue to grow with each year, possibly resulting in about three times more recharge than would occur from irrigation. The annual amount of net groundwater recharge might amount to 1,000 acre-feet or more — not bad for such a small area.

Building setback levees is expensive. A 3,400-foot-long structure and associated riparian restoration planned along the lower Feather River in Sutter County is estimated at $20 million. But in reconnecting rivers to their floodplains, these projects can yield the multiple long-term benefits of reduced flood risk, increased groundwater recharge and improved wildlife habitat.

Some communities may find this room-for-rivers approach particularly beneficial. It may be more economical to reduce flood risk by expanding floodplains rather than shore up aging levees to meet the state’s new 200-year flood protection requirement. The approach may be especially attractive to some communities — such as the San Joaquin Valley — where groundwater overdraft is most severe.

The best time to prepare for floods is before they happen. Making every drop count during a deluge can pay dividends when droughts recur and wells start to dry up.

Joshua Viers and Graham Fogg are scientists with the University of California’s Water Security and Sustainability Research Initiative.