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California’s Central Valley was once one of North America’s most productive wildlife habitats, a 450-mile-long expanse marbled with meandering streams and lush wetlands that provided an ideal stop for migratory shorebirds on their annual journeys from South America and Mexico to the Arctic and back.

Farmers and engineers have long since tamed the valley. Of the wetlands that existed before the valley was settled, about 95 percent are gone, and the number of migratory birds has declined drastically.

But now an unusual alliance of conservationists, bird watchers and farmers have joined in an innovative plan to restore essential habitat for the migrating birds.

The program, called BirdReturns, starts with data from eBird, the pioneering citizen science project that asks birders to record sightings on a smartphone app and send the information to the Cornell Lab of Ornithology in Ithaca. By crunching data from the Central Valley, eBird can generate maps showing where virtually every species congregates in the remaining wetlands. Then, by overlaying those maps on aerial views of existing surface water, it can determine where the birds’ need for habitat is greatest.

The BirdReturns program, financed by the Nature Conservancy, then pays rice farmers in the birds’ flight path to keep their fields flooded with irrigation water from the Sacramento River as migrating flocks arrive. The prices are determined by reverse auction, in which farmers bid for leases and the lowest bidder wins.

Because the program pays for only several weeks of water instead of buying the habitat, the sums are modest; the conservancy does not disclose bids because that might affect future auctions, but it says the figures were both above and below the $45 per acre that the federal government pays for bird-friendly practices.

The project’s first season ended last month, as birds headed north from newly flooded fields. Researchers said all of the birds whose numbers they hoped to improve were seen on “pop-up” wetlands – a temporary steppingstone for the birds’ journey north. This happened when the field would have ordinarily been drained, an indication that the approach was working. The fields will be flooded again in the fall for the birds’ return journey. Eventually, using this and other approaches, the conservationists hope to increase the number of shorebirds that stop in the Central Valley to 400,000, from current levels of 170,000.

BirdReturns is an example of the growing movement called reconciliation ecology, in which ecosystems dominated by humans are managed to increase biodiversity.

“It’s a new ‘Moneyball,’ ” said Eric Hallstein, an economist with the Nature Conservancy and a designer of the auctions, referring to the book and movie about the Oakland Athletics’ data-driven approach to baseball. “We’re disrupting the conservation industry by taking a new kind of data, crunching it differently and contracting differently.”

The shorebirds – among them dunlins, sandpipers, snipes, whimbrels and marbled godwits – zoom into wetlands, and wade on stiltlike legs through a few inches of water or across glistening mud flats to ferret out worms, insects, crayfish and snails with their long bills.

The Central Valley is the most developed of the landscapes they cross. Until now, one of the biggest problems has been that in February, at the peak of migration, rice farmers are letting their fields dry out in preparation for planting. “When they need it most, there’s less and less habitat,” said Mark Reynolds, a Nature Conservancy scientist who helped design the program.

In 2012 Reynolds and Brian Sullivan, the eBird project leader for the Cornell Lab of Ornithology, got the idea of using the sighting data to find out where the shorebirds go. They overlaid those data on maps of water availability in the Central Valley to determine where the needs for wetlands were greatest.

“We had a little bit of data in a few places, and on some species, but with eBird we can go wall to wall,” Reynolds said. “It’s a whole new window on migration we didn’t have before.”

The ideal depth for shorebirds is 2 to 4 inches of water; any more and it is too deep for foraging. When eBird data show that a migration is under way, rice growers who have entered low bids open their irrigation ditches to provide just the right amount of flooding. That results in the pop-up wetlands.

In this first year, 10,000 acres (out of 500,000 devoted to rice farming in the Central Valley) owned by 40 farmers were flooded for four, six or eight weeks, at an average of 200 to 250 acres each. Many farmers did not participate because of California’s drought. Even for farmers who have enough water, the program can require some careful calibration.

“If we put our water on late, the fields might not dry out” in time for planting, said Doug Thomas, a program participant who grows sushi rice. But he added that the compensation was better than adequate and that he liked the private-sector nature of the initiative.

Hallstein said that at first it was difficult to get farmers to make the shift, but that it helped when they thought of shorebird protection as just another crop, like rice. Biologists hope the approach is a solution for one of conservation’s most pressing problems.