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Judging by soil estimates, California’s three-year-old drought is its worst in five centuries. Cities from Sacramento to San Diego are seeing decreased drinking-water supply, increased wildfire risk, and no signs of relief on the horizon. The lack of rainfall forced Governor Jerry Brown to declare a state of emergency in January. And on February 14, President Obama pledged emergency money to farmers and small communities while stumping in Fresno.

But more than just people are hurting. Migratory waterfowl in California’s Central Valley, a vital stop along the Pacific flyway, depend on its wetlands for food and habitat. Without sufficient water to support these species, the birds face a host of dangers ranging from reduced food availability to the outbreak of disease.

The threat of habitat destruction looms particularly large. As the state’s agricultural heartland, over 90 percent of the natural habitat in the Central Valley has already been ceded to farmers growing a diverse set of crops, from apricots to avocados.

And since farmers and wildlife share the same water supply, the regional ecosystem is especially brittle. Any water that enters the regions has to be split between irrigation systems and the untouched wetlands, now covering just three percent of the land it once did. And it’s those wetlands migratory birds depend on.

“If conditions continue, [there could be] greatly reduced fall habitat, by one-half or more,” explains Meghan Hertel, working lands program director for ����APP California, “and little to no spring habitat for nesting birds.”

Pinpointing the extent of the harm done to bird numbers across the state is difficult. Melanie Weaver, Senior Environmental Scientist at the California Department of Fish and Wildlife, says that year-over-year population counts aren’t perfect. Measurements don’t account for variables like irregular nesting patterns or seasonal floods.

“It’s just a snapshot in time,” explains Weaver, noting that the best the dataset can do is suggest correlation, not causation. “We wish it were useful that way,” she adds.

Still, high on Hertel’s list of worries are the Tricolored Blackbird, an endangered species, and the mallard, species whose nesting colonies move into the Central Valley in the spring. Mallard numbers in California are already showing signs of decline: In 2009, the statewide count was 226,019 individuals. In 2013, that number was 202,073, according to a study by the Fish and Wildlife Service.