In years past, long-billed dowitchers flying in from Alaska could count on California stopovers to offer vast stretches of fresh melted snow teeming with plants and insects.

But now, as the Sierra Nevada snowpack has vanished and clouds offer little rain, few lush sanctuaries are available to sustain these shorebirds on their journey along the avian highway known as the Pacific flyway. Experts say that once the dowitchers arrive in the Central Valley this month, their prospects look bleak.

Along the 4,000-mile-long Pacific flyway—one of four main routes in North America for migrating birds—up to six million ducks, geese, and swans wing south every year to find warmth after raising young in the rich habitats of Alaska, Canada, and Siberia. They are joined by millions of shorebirds, songbirds, and seabirds, including the ultimate endurance winner, the arctic tern.

But California's drought has dried up its wetlands. Many insects, fish, and plants are gone. As a result, some migrating birds have died or been depleted of so much energy that they have trouble reproducing. Thousands of ducks and geese, crowded onto parched rivers and marshes, are felled by botulism and cholera, which race through their feeding grounds. ( Read about how freshwater fish are also suffering. )

Waterfowl Pacific Flyway California’s water shortage affects the Pacific flyway, but no two drought stories are alike. A close look at the Lower Klamath National Wildlife Refuge and the Central Valley, from the Sacramento Valley to the San Joaquin Valley, reveals what contributes to bird success and failure during a dry spell. LAUREN E. JAMES, NG STAFFSOURCE: Nature Conservancy

Drought and deluge are part of the natural cycle of life in California. But species that have migrated for thousands of years on the same routes since glacial sheets melted at the end of the Pleistocene now struggle to adapt to human-managed water supplies in the backdrop of a globally changing climate that exacerbates dry spells. ( Read about how California’s drought veterans are coping. )

"The longer droughts are the worst. At first, the energy deficits from too little food affect the weaker or younger ones. In back-to-back droughts, even the strong birds get pushed to the limit," says Blake Barbaree, an avian ecologist at Point Blue Conservation Science, a nonprofit research center in Petaluma, California.

A Mere Trickle

The Pacific flyway cuts through interior California and along the state's coast, through habitat that has vastly changed after four years of severe drought and decades of water diversions.

Sandhill cranes and greater yellowlegs flying from Anchorage, Alaska, will reach the Kern National Wildlife Refuge near Bakersfield only to find a mere trickle.

Tricolored blackbirds, which live only in California, have traded permanent marshes for farm fields where nests are destroyed during harvests. Numbering in the millions a half century ago, the San Joaquin Valley's tricolored blackbirds plummeted by around 75 percent since 2011, triggering an endangered listing by the state last December.

The eastern Sierra's shrinking Mono Lake, destination stop for Wilson's phalaropes and tundra swans, dropped three feet of depth during the past four years. Southern California's inland Salton Sea, visited by pelicans and dozens of other species, suffers as its water pipe from the tail end of the Colorado River provides less and less. Starving young Cassin's auklets, hatched on the Farallon Islands, washed up dead on beaches in the tens of thousands after ocean waters warmed to the point that krill moved too deep for the seabirds to catch.

Western sandpipers, weighing around one ounce, that migrate from Alaska to the Central Valley usually stop for one or two days on the Oregon border in the Klamath Basin, the "Everglades of the West," to feed and rest. But last year, many had to keep moving, says John Takekawa, a former U.S. Geological Survey biologist who has a new science position with the National Audubon Society.

Less Water Means Fewer Birds As drought depletes the water supply in the Lower Klamath National Wildlife Refuge, migrating birds seek sustenance elsewhere. Fewer birds stop at the refuge in drier years. Water supply has also shifted by season over the past 15 years. Now with the dwindling mountain snowpack, most waterfowl visit the LKNWR in the spring. By the fall, the refuge has run dry. Waterfowl Accumulated millions of birds visiting the refuge each day Water Thousands of gallons an acre EMILY M. ENG, NG STAFF; VICTORIA SGARROSOURCE: Fish and Wildlife Service

"Having the right resources at the right place at the right time is key to their success," Takekawa says. "There are so few areas that they can stop."

Most scientists suspect—although it's hard to document—that there's a carryover effect when a bird can't get food in one part of the flyway: Fitness is diminished and, with it, the chance of breeding, Takekawa says.

"Quite a Sad Scene"

The drought's effects are staggering at some major stops. In the generous water year of 2012, Barbaree and other Point Blue scientists counted 4,000 long-billed dowitchers in one wetland in the Klamath Basin. The dowitchers stayed for at least 30 days that July and August, feeding, resting, and molting, before moving on to the warmer Central Valley.

But then, in 2013, after Indian tribes claimed senior water rights to sustain salmon runs downstream, the Lower Klamath National Wildlife Refuge went dry. For six weeks in August and September, the refuge, which is typically filled with thousands of western sandpipers, greater white-fronted geese, snow geese, and northern shovelers, stood desolate. "It was just quiet and dusty. There was not a drop of water," Barbaree says. "It was quite a sad scene."

The dowitchers and other birds crowded into the upper Klamath River, searching for food. Avian botulism, a disease born of bacteria, set in. "We were having to step over birds that were slowly dying," he adds. "They couldn't fly. They couldn't swim. It was hard to see." Mallard ducks, flightless during molt, had no way to escape the botulism.

Again last year, the Klamath Basin, larger than Maryland, was starved for water. Supply for the basin's refuges is expected to be near nil again this summer. The refuges fall in the bottom tier of water rights holders, and legislation encompassing a 2014 water agreement that could increase the supply awaits action by the U.S. Congress.

Preparing for This Year's Migrants

Farther south, in the heart of the Central Valley, the Sacramento National Wildlife Refuge saw the same crowding scenario last year, says Dan Frisk, who manages the complex of five refuges about 70 miles north of Sacramento. This year, there may be fewer growers planting rice and flooding their fields, depriving waterfowl of even more food and water.

Last year was "a real eye-opener," he says. Water allocations to those areas were cut by 25 percent, the same percentage as agriculture. Frisk had to decide when to ask for water from nearby Shasta Lake Reservoir. He's working with growers, private landowners, and environmental groups to find any water he can. "We didn't produce enough food last year. We're doing more early irrigation this year to prepare for those birds coming in," Frisk says.

First last August come the iconic northern pintail, an elegant duck, with its needle tail and long, slim profile. "You start seeing these big flocks of snow geese and Ross's geese. It's quite spectacular. The skies are full of birds. When we're flooding up the water grass, the insects are pushed up. It's a feeding frenzy on a smorgasbord of food," Frisk says.

How the Waterfowl Habitat in the Central Valley Is Disappearing Wintering waterfowl in the Central Valley rely on three major habitat types: managed seasonal wetlands that are flooded in the fall, rice fields that are flooded after harvest (winter-flooded rice fields), and harvested cornfields. A 59 percent habitat loss diminishes waterfowl food supplies by 33 percent to 50 percent, depending on the habitat type. In acres per year Winter-flooded rice fields Planted grain corn Managed wetlands EMILY M. ENG, NG STAFF; VICTORIA SGARROSOURCE: Mark Petrie, Ducks Unlimited

The Sutter Bypass Wildlife Area in the Sacramento Valley was dry last year until a short burst of December rescue rain, and Frisk worries about what will happen this year.

"The birds will see there's no water and will fly to where water is. Now there's one less refuge and pressure on the other refuges. When they fly back to breeding territory in Alaska and Canada, they're not in good shape. If they're weak, they're susceptible to disease. Some may not breed," Frisk says.

Ducks Can't Get Enough Food in the Central Valley Under normal water conditions, Central Valley habitats satisfy duck energy requirements, except in late March. A sharp decrease in flooded habitats in the fall exhausts food supplies by midwinter, when duck populations peak. Energy in billions of kcal Normal Water Conditions 2015-2016 Predicted Drought Conditions Demand is based on population objectives and the energy requirements of individual birds. Energy supply is based on foraging habitats and the food biomass and nutrition they contain. EMILY M. ENG, NG STAFF; Victoria SgarroSOURCE: Mark Petrie, Ducks Unlimited

Along the coastal part of the Pacific flyway, on the last day of April, Josiah Clark, a champion birder, pedaled 130 miles, from the Santa Cruz Mountains to San Francisco Bay, in 24 hours with a fellow birder, Rob Furrow. They saw 187 species, setting a Northern Hemisphere record for a birding-on-bicycle competition. But the vegetation looked dry like June instead of wet like spring, Clark says.

They saw cinnamon teal and hummingbirds near the coast rather than inland, and western sandpipers and dunlins were switching to kelp flies on the beach instead of insects in a flooded meadow. "It shows their resilience," Clark says. "Those birds that don't figure it out are not going to pass on their genes," which ultimately can determine evolutionary success or failure.

Restoration Offers Hope

Among the dire conditions, some hope arises: In times of drought, work to restore diked shoreline and salt works back to tidal marsh and shallow ponds is paying off for birds. Last December, as the San Francisco Bay waters washed over breached dikes to reclaim dry ranchland, the pintails, wigeon, canvasbacks, and ruddy ducks came careening in, says Joy Albertson, manager of the Don Edwards National Wildlife Refuge.