The five-year-drought could hardly have been worse for some of California’s fish populations. The Sacramento River’s winter-run Chinook, for example, were nearly extinguished by low water supplies and sloppy handling of reservoir releases during the endangered salmon’s spawning season. The delta smelt, too – a key biological indicator species – is now closer to extinction than it has ever been. On the Klamath River, potentially deadly parasites that thrive in low-flowing rivers infected most of the Chinook born in 2014 and 2015.

After weeks of heavy rains and a mounting snowpack in the Sierra Nevada, California’s drought is easing, and according to the U.S. Drought Monitor, Northern California is drought-free. That should be good news for fish.

“All this rain is definitely a good thing,” says Dave Hillemeier, the director of the Yurok Tribe’s fisheries department. He says fast, gushing flows could potentially wash out of the river system a species of worm that serves as a host to the problematic fish-killing parasite Ceratonova shasta, which has been linked to population declines of Klamath steelhead and salmon.

“One day of huge flows would make life miserable for these polychaete worms,” Hillemeier says, explaining that rapid currents can not only sweep away the creatures themselves but also the algae on which they feed.

In the Central Valley, high flows are also a boon to fish, especially when rivers spill their banks. Research has consistently shown that numbers of young fish spike in the months following wet winters – probably because they create valuable, if only ephemeral, floodplain habitat for the fish.

However, too much rain at once can spell trouble for a river and its fish. High flows can wash away gravel beds containing incubating eggs – what biologists call “scour.” Rapid increases in flow can also bury and suffocate eggs with fine sediment or even sweep young salmon prematurely out to sea. These impacts are especially problematic in river valleys that have been overhauled by human activities such as logging, levees, dams and development.

“It’s not that the salmon aren’t able to tolerate droughts and floods,” says Eric Ettlinger, aquatic ecologist for the Marin Municipal Water District. “It’s that their habitat has been so altered that the rivers don’t work the way they should anymore.”

For example, Lagunitas Creek and its lower tributaries, which flow off the highlands of western Marin County, have been lined with bank fortifications and berms that confine the streams to their main channels. This looks tidy and effective from a land use perspective, but it makes the fish that live in the river extremely vulnerable to flooding as well as drought. That’s because water that overflows a river’s banks creates slow-moving sprawls of habitat – perfect places for young fish to take refuge from the raging currents that may scour out the main channel. Such overflow also creates groundwater recharge, which feeds into streams and can keep them flowing through months, or even years, of drought. Eliminating natural flooding cycles eradicates these ecosystem benefits.

Dams have introduced other challenges for Lagunitas Creek’s coho (a member of the salmon family). The barriers prevent the fish from spawning in the watershed’s high headwaters, where the salmon historically laid and fertilized their eggs. Such small creeks, Ettlinger explains, are far less susceptible to the scouring effects of flooding than the lower reaches of the system, where tributaries merge together and create gushing torrents during rainy periods.

Today, Lagunitas Creek’s coho are barely clinging to existence, and the wet winters that should be so welcomed can actually have drastic negative impacts on the population. In the winter of 2005–06, heavy rains coincided with the egg incubation period of the stream’s coho. The number of spawning adults crashed from roughly 400 to just 50 in the space of two years. Ettlinger guesses the fish, 600 spawners strong at last count, will take a similar hit this year.

Ted Sommer, a lead scientist with the California Department of Water Resources, says 1,800 Chinook salmon spawned last fall in Putah Creek, a Sacramento tributary with headwaters in Napa County. It was one of the largest returns in memory.

But Putah Creek, like so many rivers, has been channelized with riverbank modifications. This, Sommer says, “creates a fire-hose effect as water shoots straight down the river channel,” and he believes many or most of the incubating salmon eggs have been lost to the heavy flows of December and January.

However, few examples so clearly show the potential of heavy rains to devastate rivers as the North Coast’s 1964 Christmas floods. That December, the Eel River – in recent years just a trickle of water – exploded to one-and-a-half times the average volume of the Mississippi. Towns were swept away, and redwood trees that had grown for a thousand years were stripped from the earth.

Erosion was cataclysmic on recently logged mountainsides, says Scott Greacen, executive director of the group Friends of the Eel River.

“When you take the trees off those slopes, the earth’s surface melts,” he says. “When those rains fell, the mountains just came unzipped.”

Rocks and sediment buried river sections where fish spawned. In some places, pools that were 80ft (24m) deep and provided valuable year-round cold water – essential for salmon – were filled in with rocks and sand.

“The river was structurally altered,” Greacen says.

The same rainstorms clogged and buried parts of the Klamath River and its main tributary, the Trinity. Greacen says a local geologist told him that it might take 7,000 years for natural processes to erase – and quite literally wash away – the effects of that rainy winter.

Fishery biologist Jacob Katz, of the group California Trout, has spent years studying the benefits floodplains provide for fish. His work has been focused recently on the Sacramento River. He and other scientists attribute the long-term decline of the Central Valley’s wild, self-sustaining salmon populations in large part to the levees that have disconnected the river from its adjacent floodplains. Today, those agricultural flatlands flood only during extreme weather events, whereas they used to be inundated most, if not all, years.

Katz’s research has all but proven that salmon cannot survive without annual flooding. He acknowledges the impacts that floods can deliver to some rivers, especially those stripped of the protective wetland and woodland buffers that soak up runoff and release it slowly and gently into the river.

Overall, however, Katz says the benefits of precipitation far outweigh the impacts.

“It’s years like this one that it’s good to be a salmon in the Central Valley,” he says.

Never miss an update. Sign up here for our Water Deeply newsletter to receive weekly updates, special reports and featured insights on one of the most critical issues of our time.