Populations of salmon-killing parasites on the Klamath River appear to be growing in recent years, and scientists are trying to get a grip on why the problem is becoming so severe.

In the past five weeks, biologists have been sampling juvenile chinook salmon and finding many of them infected with one or two parasites. One hits the fishes' digestive tract, the other their kidneys.

While some suspect low flows and warm, poor-quality water are making the fish more susceptible to the parasites, scientists are just beginning to understand the scope of the problem. Some say the Klamath River is a system so out of whack that the parasites have begun to flourish in ways not common in parasite-host relationships.

U.S. Fish and Wildlife pathologist Scott Foott said it appears the high rate of infection this year is a result of an exceedingly high dose of the parasites.

The first parasite is Ceratomyxa shasta, which has been known to infect between 12 and 40 percent of juvenile salmon in recent years. The other is Parvicapsula minibicornis -- which has in the past been found in nearly all juvenile salmon. This year, some 63 percent of the little fish are thought to be affected so far.

Foott could not say whether the die-off compares to the 2000 juvenile fish kill, when an estimated 200,000 succumbed to the diseases.

C. shasta's intermediate host is a freshwater worm, and a similar host may hold P. minibicornis, though pathologists aren't sure.

While both crop up along the length of the river, the problem appears most acute in the area just below the Klamath's lowermost dam, Iron Gate.

"We're thinking that the hot spot for infection is probably in the upper reaches," Foott said.

Foott said he doesn't know why. But he said some have suggested that the Klamath's flows are crimped by irrigation and hydropower at critical times of the year. Winter and spring flows may have previously scoured many of the intermediate hosts from the river, the hypothesis goes.

A graph of the river's historic flows -- still a disputed topic -- generated from information by the National Marine Fisheries Service, shows a bell-shaped curve. After the dams were built on the Klamath, the graph shows more water coming down in late fall and winter, only to be cut back in the spring when water for the federal government's upstream Klamath Irrigation Project is stored.

Foott said scientists may have missed a chance to study how big winter and spring flows affect the abundance of the parasites in 1997 and 1998, an el Niño year that dumped huge amounts of rain and snow in the watershed.

Just two years later, though, more than 200,000 infected juvenile salmon died in the river.

Portland, Ore.,-based PacifiCorps' hydropower dams also alter the river's flow regime. The reservoirs behind the dams also act to enrich nutrients and warm the already poor-quality river water let loose from Upper Klamath Lake.

That sparks algae blooms that turns the water alkaline and drops the amount of dissolved oxygen in the lakes, according to research done by the Klamath Basin Tribal Water Quality Work Group.

Salmon get stressed in such conditions, making them vulnerable to diseases. California and Oregon water quality officials have said the conditions are unacceptable.

In contrast, the disease rate in Klamath tributaries like the far-cleaner Salmon and Trinity rivers are markedly lower.

PacifiCorps six dams now in the federal relicensing process, and lower river proponents are pushing for a major investigation of the facilities' effects on water quality.

'Serious problem'

This year was declared a dry year by the Reclamation Bureau. That was a change from the initial "below average" forecast, which would have allowed more water down the river. Through a multimillion-dollar water bank, Reclamation is supplementing the flows this spring.

Reclamation spokesman Jeff McCracken said there is another 10,000 acre feet -- 3.25 billion gallons -- available should state and federal wildlife agencies request it. He said the bureau hasn't heard anything from the agencies to date.

The California Department of Fish and Game is still mulling over whether to use the water. While flows were cut back on Tuesday, and water temperatures are climbing, Fish and Game Fisheries Program Manager Gary Stacey said the relatively small amount of water might not do any good.

"There's not a whole heck of a lot of water to go around," Stacey said.

If water temperatures climb high enough to force the several million young fish in the system to crowd into the cooler mouths of tributaries, Stacey said, things could get worse. Temperatures above 70 degrees can cause the parasites to multiply rapidly, especially in crowded conditions, putting heat-stressed fish at even worse risk.

Water temperatures at Klamath Glen hit 68 degrees on Friday.

Fishermen are concerned that strung together, the 2000 fish kill, the 2002 adult fish kill that claimed 34,000 salmon, a spring die-off this year and another potential adult fish kill this fall could put the brakes on commercial, sport and tribal harvest.

The 2002 fish kill was caused by a protozoan infection commonly called ich and a bacterial infection called columnaris. Fish and Wildlife found that low, warm water held up migration of the fish in the lower river, leaving them prone to infection.

"There's a serious problem in that basin," said Eureka commercial fisherman Dave Bitts. "The signs are not good."

He said Reclamation is ignoring a key element: That its operations are set up to prevent harm to threatened coho salmon, not chinook, which spend more time in the main channel of the river.

The National Research Council, in its report on the Klamath, held the same view.

As biologists try to piece together the disease complex, they are also faced with the reality of inconsistent funding. Foott said scientists need to figure out why C. shasta, for example, isn't found in Klamath tributaries even though its spores are released after spawning fish die.

"It's not a well-funded effort at all," he said.

Reclamation may be beginning to feel the importance of the issue.

McCracken said the bureau is exploring the possibility of further funding state, federal and tribal efforts to monitor the problem.