Noah’s Ark supposedly provided shelter to animals from the rising floodwaters. But at a federal breeding site near Shasta Lake, Calif., the opposite is occurring: The tanks of Livingston Stone National Fish Hatchery are providing refuge this summer for salmon nearly out of water. There, staffers are rearing the only insurance policy that the Sacramento River’s winter-run Chinook have against extinction: a living genetic bank of 1,035 baby fish, selected to reseed the population should it extinguish in the wild. Unique coloring, genetics and size distinguish this subspecies, which is protected under the Endangered Species Act.

The Golden State’s extreme drought, now well into its fourth year and said by climate scientists at the University of Minnesota and Woods Hole Oceanographic Institution to be the state’s worst in more than 1,200 years, has been accelerating the anticipated demise of several of California’s endangered fishes, including its salmon. A total of five species and subspecies of the state’s salmon, along with lesser-known native fish species such as the delta smelt already were imperiled by decades of habitat loss caused by the region’s dams and water withdrawal for human use. Just last month the National Oceanic and Atmospheric Administration (NOAA) named central California coast coho and the Sacramento River winter-run Chinook as two of the eight endangered species in the U.S. “most at risk of extinction”. With the dry climate, over half of the stream gauges in California are measuring water flows less than one tenth the normal rate this month, according to the U.S. Geological Service. A state trawl survey for the delta smelt this past spring turned up just one of these silver-blue bait fish in the entire Sacramento–San Joaquin Delta watershed. Other endangered species, such as the Red Hills roach and Owens tui chub, are being confined to smaller and smaller refuges of water as their native creeks and streams dry up. (The former is currently confined to a 250-meter stretch of spring-fed Horton Creek, west of Sonora.) “As far as I’m aware of nothing has gone extinct but I have my fingers crossed,” says Peter Moyle, a University of California, Davis, fish and conservation biologist. “This summer is really going to push these systems to the limit.”

Last summer the winter-run Chinook experienced catastrophic spawning failure on the Sacramento River, thanks to shrinking and warming water habitat from the drought. “Somewhere between the egg stage and what’s called the fry stage (five- to 10-week-old juveniles), they just cooked,” says Sean Hayes, lead researcher of NOAA’s Salmon Ocean Ecology Team. It’s estimated that 95 percent of the winter-run Chinook eggs and fry died last year. Eric Danner, a research ecologist with NOAA, is not optimistic about the survival of this year’s salmon eggs and fry either “given that we’re in another year of the drought and the water conditions in the reservoir [Shasta lake] are worse than they were last year.”

Not only is California dry, it’s also hot. So far, 2015 is the state’s warmest year on record (with 2014 in second place). Record-breaking air temperatures are exacerbating the drought’s severity by reducing snowpack and increasing the evaporation of water from the soil. The warmer air temperatures also heat lakes and rivers (which are already dwindling in size due to the drought) further reducing the cold water available for salmon, which have strict temperature thresholds for survival.

The Sacramento River’s winter-run Chinook were once a pillar of the Central Valley’s storied and historic salmon runs, which fed the 1849 gold rush and produced most of state’s salmon. With the completion from 1945 to 1950 of Shasta and Keswick dams on this river, the salmon were cut off from their historic spawning grounds in upstream tributaries, the spring-fed Shasta and McCloud rivers, where the waters always ran cool. Blocked by the impassable dams, the fish began to spawn in the main stem of the Sacramento River downstream of Keswick Dam, where the water, sourced from Shasta Lake (California’s largest reservoir), was the coolest that they could access. To help further reduce water temperatures downstream of the dams, the Bureau of Reclamation retrofitted Shasta Dam with a temperature control device, which allowed dam operators to draw water from different depths of Shasta Lake (the deeper the water, the colder it is) to create a cold water habitat for downstream fishes, including the river’s salmon.

The more snowmelt feeding into a reservoir, the colder its water, and the deeper the water levels in a reservoir, the more cold water it stores. Only now with the drought, water levels in Shasta Lake have dropped to the point that there simply isn’t enough cold water left to be released by dam operators for the salmon downstream. Salmon are cold-blooded and if the water they’re in becomes too warm, they die. For the Chinook, the ideal temperature for the successful incubation of eggs and survival of fry—a critical six-month-long window—is between 9 and 10 degrees Celsius, with 13 degrees Celsius as the maximum targeted temperature that any eggs would be exposed to. In most years water managers have been able to keep water temperatures along a 15- to 50-kilometer section of the Upper Sacramento River immediately downstream of Keswick Dam, where the winter-run Chinook spawn, below that 13 degrees C threshold throughout the summer and fall by releasing a steady flow of cold water from Shasta Lake. But last August, with water levels in Shasta Lake at 30 percent capacity, water managers lost temperature control of the river below in the dam through to October.

The loss, which saw river water temperatures spike to 16.5 degrees C, occurred exactly during the season that baby winter-run Chinook were incubating in the river’s gravel beds. “It’s probably when they’re most susceptible to water temperatures, so it’s the worst possible time to have elevated water temperatures,” says Jason Roberts, fishery supervisor with the California Department of Fish and Wildlife. Federal and state fisheries biologists estimate the warm water killed 95 percent of 2014’s winter-run eggs and fry. Of the remaining 5 percent that survived the warm water, NOAA’s Hayes thinks it’s unlikely that many survived the nearly 500-kilometer-long journey to San Francisco Bay, where they head out to sea for two to three years before returning to the Sacramento River to spawn and die. Warm water temperatures raise the body temperatures and metabolisms of predatory fishes in the river, so they need to eat more. “The warmer water is just making hungrier predators in these [salmon] that are already physiologically stressed, so they have to navigate through these minefields,” Hayes says. To add insult to injury, any fish that manage to make it to the ocean will be met by especially poor ocean conditions, thanks to a particularly strong El Niño signal that is expected to persist through this coming winter and into next spring. In other words, the candle is burning at both ends for the winter-run Chinook—out at sea, where they grow to maturity, and at their spawning grounds, where their three-year life cycle is supposed to begin anew. At this rate, the winter-run Chinook look to become the first of the state’s native fishes to be driven to extinction from the drought.

Before it was too late, hatchery staffers last year rescued 1,035 wild Chinook salmon fry to create a captive broodstock that would be reared in tanks for breeding. The idea is to safeguard the bloodline of California’s endangered winter-run Chinook salmon against the drought’s devastating and possibly terminal toll on the population. The specimens were selected for their genetic diversity. “We’re hoping that in three years half those fish will survive and we’ll still have 250 females and 250 males,” says John Rueth, assistant hatchery manager at Livingston Stone. At that point they would be bred to produce offspring, which could be reintroduced to the Sacramento River should the winter-run Chinook go extinct in the wild. In addition to the broodstock program, the hatchery also rears and releases artificially bred winter-run Chinook into the Sacramento River to help restore the population to its historic levels. This year, because of the drought, the hatchery has tripled its production of these hatchery winter-run Chinook in an effort to offset the expected loss of natural production in the river this year. “All the agencies basically got together and said, let’s take these fish into the hatchery, because we know they survive better in the hatchery than out [on the river] and that way we won’t have one of these terrible years where there’s no production in the wild of winter-run Chinook,” says Rueth, who sees the hatchery as a refuge for the fish, helping to keep their population going through this deadly time. “We’re sort of the last defense for what’s out there right now.”