Key salmon spawning rivers all but dry

The key spawning grounds for what was once the greatest run of salmon on the North Coast are close to being as dry as they have ever been, according to biologists and the U.S. Geological Survey.

As California bakes under a third year of drought, the Scott and Shasta rivers, near the California-Oregon border, have become little more than dry beds of rock and dirt.

Recent measurements showed the water volume in both rivers approaching record lows for this time of year. The two tributaries of the Klamath River are historic breeding grounds for salmon and are considered critical to the recovery of the species.

"Large areas of the (Scott) River have gone completely dry, stranding endangered coho salmon as well as chinook and steelhead in shallow, disconnected pools of water," said Greg King, president of the nonprofit Siskiyou Land Conservancy, which has fought to protect the salmon runs in the Klamath River system.

"This could be the year that causes the coho to go extinct if they can't get upstream in the Scott and Shasta."

Salmon once abundant

The Klamath River system, historically the third-largest source of salmon in the lower 48 states behind the Columbia and Sacramento rivers, once supported hundreds of thousands of wriggling chinook salmon, coho salmon and steelhead trout. Chinook once swam all the way up to Klamath Lake in Oregon, providing crucial sustenance to American Indians, including the Yurok, Karuk and Klamath tribes.

The teeming salmon runs were so abundant that old-timers remember being awakened at night by the sound of thrashing fish. Legend has it the big spawners were so crowded together that they could be harvested with a pitch fork during peak season.

Their numbers began declining in the mid-20th century as a result of dams, agricultural irrigation and logging. By the mid-1980s, only a few thousand fish were left - mostly on the Scott and Shasta.

The number of salmon now in the river is a tiny fraction of what it was a century ago, and California coho are listed as endangered - which is why the water level in their breeding grounds is so important.

The U.S. Geological Survey gauge on the Scott River near Snow Creek measured an average water volume of only 5.1 cubic feet per second on Aug. 30, with a low that day of 3.5 cfs.

That's compared to the median flow of 47 cfs on that date based on 67 years of measurements. The lowest average volume recorded in one day on the Scott was 3.4 cfs on Sept. 20, 2001. Measurements are recorded 96 times a day.

A flow of 3 cubic feet per second is the equivalent of 22.44 gallons of water rolling between the banks. In an average-size riverbed, it is barely a trickle.

Shasta River levels

The Shasta River hit a low daily average of 5.0 cfs on July 29, dipping that day to 3.0 cfs near where it empties into the Klamath.

The record low for the Shasta was 1.5 cubic feet on Aug 24, 1981. The normal flow on the Shasta at this time of year is between 25 and 30 cfs based on more than 70 years of data.

Al Caldwell, the geological survey's deputy chief of California's hydrologic monitoring program, said river volumes fluctuate wildly, so it is impossible to get a complete picture until the season averages are calculated. Although the flows increased slightly this past week - possibly as a result of less irrigation by farmers along the banks - Caldwell said water levels overall are still abysmally low.

"The important thing here is that we are very close to a minimum of record at the Scott River," Caldwell said. "We're practically at the minimum on the Shasta River and if it continues to go down we'll break the record."

Troubling time

The situation is particularly troubling for anglers, Indian tribes and environmentalists given the dismal state of the California fishery. Devastating declines in the number of spawning salmon in both the Klamath and Sacramento river basins forced regulators to ban almost all ocean fishing of chinook salmon in California and Oregon for the past two years.

The Scott and Shasta rivers are important not just as spawning grounds, but because the two tributaries are a main source of cold water for the Klamath, which is having terrible problems with algae blooms associated with warm, pooling water.

Low water isn't just a problem on the far North Coast. A declining snowpack has meant the Russian, Eel, Napa, Salinas and Gualala rivers and many tributaries around the state are hurting for water. But it is a particular problem along the Klamath, where the consequences are comparatively dire.

Environmentalists and local Indian tribes have been fighting for years to stop water diversions for irrigation. In 2002, 33,000 fish went belly-up after the Bush administration slashed releases to the river.

Still, ranchers exercising water rights adjudicated in the 1930s typically lower the rivers by sucking up groundwater during the summer.

"It's been a chronically bad problem," said Pat Higgins, a fisheries biologist who works for five lower basin Indian tribes on water- and dam-related issues. "It's worse this year than it has been in the last 10 years."

Restoration work

But there has been progress. Over the past decade, many ranchers have joined efforts to screen agricultural pump intakes to avoid sucking in baby fish. They've also made efforts to stop soil erosion, which can silt up rocky spawning grounds, and restore shady riverside forests that help lower water temperatures. Some help transport fish trapped in "dewatered" streambeds.

Negotiations are under way between U.S. Interior Secretary Ken Salazar and the various stakeholders to remove four small dams - Iron Gate, Copco I, Copco II and J.C. Boyle - built on the Klamath starting in 1909. The enormously complicated deal would restore 300 miles of spawning habitat.

But the dams probably won't be removed for another 12 years. With the expectation of at least one more month of hot, dry conditions, time may be running out.

"Until you fix the passage problem and take out the four dams, it's those tributaries where we really ought to be focusing our restoration efforts," said Chuck Bonham, the senior attorney for Trout Unlimited in Berkeley. "We're going to have to round the corner here and start doing the tough stuff."

For a USGS graph showing flows in real time, go to links.sfgate.com/ZIBY or links.sfgate.com/ZIBZ.

E-mail Peter Fimrite at pfimrite@sfchronicle.com.