The lowest number of chinook salmon in recorded history made their way up the Sacramento and San Joaquin rivers last fall, turning what was already a disaster for the fishing industry into what some are calling an environmental and economic catastrophe.

It is the second year in a row that there have been record low numbers of spawning salmon, a situation that has created a political conundrum as the battle among farmers, fishermen and various municipalities over water rights heats up.

Only 39,530 fall-run chinook spawned in the once-thriving salmon factory known as the Sacramento-San Joaquin River system. That's compared with 64,456 in 2008 and 87,940 the year before that. It is the worst three-year period in the watershed since records were first compiled in the 1970s, biologists said.

"It is bad," said Michael O'Farrell, a fisheries biologist for National Oceanic and Atmospheric Administration fisheries service. "This is the lowest number of adult spawners that we have observed in the Sacramento system and it is continuing a three-year pattern of decline. Certainly we're going to take a very close look at this situation."

Neither O'Farrell nor biologists with the California Department of Fish and Game could explain the low numbers, which fell well short of the 122,196 fish that scientists had predicted would show up.

"The collapse of the fall-run chinook population and fishery is a catastrophe for fishermen and for those who like to see our streams full of salmon, as they were only a few years ago," said Peter Moyle, a nationally known UC Davis professor of conservation and fish biology.

Fishing ban likely

The 14-member Pacific Fishery Management Council has banned ocean salmon fishing off the California and Oregon coasts two years in a row because of the paltry numbers. There is little doubt, given the situation, that the fishing ban will be extended a third year when the council meets in March and April to determine fishing limits.

"It is devastating to see a number like this," said Dick Pool, a fishing equipment manufacturer and the Western regional director of the American Sportfishing Association. "When we look to the future, it really portends trouble for these fish."

The Sacramento River's spawning run was the last great salmon run along the giant Central Valley river system, which includes the San Joaquin, American, Feather and Yuba rivers. In these waterways were leaping, wriggling chinook so plentiful that old-timers recalled reaching in and plucking fish right out of the water.

Chinook, known scientifically as Oncorhynchus tshawytscha, hatch in rivers and streams. Also known as king salmon, they pass through San Francisco Bay and roam the Pacific Ocean as far away as Alaska before returning three years later to spawn where they were born in the Sacramento River and its tributaries.

The fall run in September and October has for decades been the backbone of the West Coast fishing industry, providing 90 percent of the king salmon caught in California and 60 percent harvested in Oregon. At its peak in 2002, 769,868 fish spawned in Central Valley rivers.

Poor ocean conditions

A study last year by federal, state and academic scientists blamed most of the collapse on poor conditions in the ocean. The destruction of river habitat, water diversions and dams in the Central Valley weakened the fish and they couldn't handle the scanty food supply in the warming Pacific Ocean, according to NOAA scientists.

Exacerbating the problem, some researchers claim, is the fact that most of the salmon in California are now less genetically diverse hatchery fish instead of naturally spawning wild chinook.

The dismal return is threatening to inflame tensions between California farming interests and the fishing industry. Moyle and others said ocean conditions have improved over the past few years, so salmon numbers should have increased. That has, in turn, fueled the contention among fishing representatives that diversions of water from the delta for agribusiness are causing the problem.

Fishermen were furious this week when Sen. Dianne Feinstein proposed diverting more water for Central Valley farmers. They claim she is being bamboozled by agribusiness interests and right-wing talk show hosts who insist cuts in water exports are putting salt-of-the-earth farmers out of business.

The real story, Pool contends, is that reckless increases in pumping have sucked up and killed millions of baby salmon as well as delta smelt, the tiny endangered fish that Fox News pundit Sean Hannity and agricultural lobbyists referred to as the "minnow" environmentalists are hosing farmers to save.

"We're watching our salmon disappear in exact concert with a 16 percent increase of delta water diversions over the last decade," Pool said.

Fishing jobs lost

Whatever the cause, an estimated 23,000 fishermen and fishing industry workers have lost their jobs as a result of the fishing ban. About 1,200 commercial boats have been grounded during salmon season while harbor communities and fishing-related businesses have lost an estimated $2.8 billion.

O'Farrell said an advisory body of scientists will be investigating the cause of the decline.

"Of course, we all wish there were more fish," he said. "No one is happy."