Chris Caskey, The Union Democrat

The number of salmon running up the Stanislaus River during the fall has increased in recent years, studies show.

This time every year, Chinook salmon run from the ocean up the tributaries of California's major rivers, the Sacramento and San Joaquin, to spawn. The fall run feeds the Pacific Ocean salmon population and is celebrated every year with local festivities.

The Stanislaus River Salmon Festival will be held Nov. 3 in Knights Ferry near the salmon spawning beds and the Tuolumne River Trust will organize paddling trips on the first two weekends of November passing spawning grounds on the Tuolumne River.

It appears those events will celebrate a robust year for the anadromous fish, which saw their populations along local rivers decline dramatically for years up to about five years ago.

Since then, populations in the San Joaquin River basin have been trending upward, said Doug Demko, a biologist who runs FISHBIO, a group of research scientists, engineers and technicians who specialize in counting, tracking and analyzing trends in fish and wildlife populations throughout the world.

This year's fall run has already seen 2,179 Chinook salmon pass a weir set up near Riverbank on the Stanislaus River, Demko said. According to FISHBIO statistics, counts at the weir didn't even reach 1,000 in 2007 through 2009. Headquartered in Oakdale, the company tracks the salmon population along the Stanislaus River for the Oakdale Irrigation District, Tri-Dam Project and South San Joaquin Irrigation District.

Demko said on Wednesday that if the run continues at this year-to-date rate, it will be the strongest fall salmon run on the beleaguered river in a long while.

"For the most part, the trend is pretty consistent," he said.

Chinook salmon run up rivers to spawn throughout California, although the Central Valley populations that historically lay their eggs in the state's mountain streams have overall seen their numbers decline over the past century, according to the California Department of Fish and Game.

The fall run of San Joaquin tributaries like the Stanislaus, Tuolumne and Mokelumne usually begins in September or October and continues through December. The peak migration usually occurs in November.

The mature fish, having spent two to five years in the ocean, return to lay eggs in the gravel beds of their freshwater birthplace only to die after spawning. The eggs typically hatch 60 to 90 days later, with the juveniles swimming out to sea.

According to the California Department of Fish and Game, the fall run of the Central Valley salmon - usually the biggest run - once numbered in the millions. That number declined over the years, though included some cyclical bumps, until dipping below 100,000 in 1990 and reaching only 66,000 in 2008 for the entire Sacramento-San Joaquin river system.

Experts believe reasons vary for the steady decline. According to Fish and Game, over-fishing in the ocean, pollution in the Sacramento-San Joaquin Delta, dams along the state's rivers and reduced flows are all cited as causes.

State and federal legislators have made moves since the 1990s to try and improve the populations.

The 1992 Central Valley Project Improvement Act increased water flows for salmon ecosystems. Ongoing plans for the Delta are looking to balance salmon population concerns and environmental factors with the state's water supply needs.

In 2008 and 2009, a controversial order banned commercial salmon fishing in California coastal waters.

Rhonda Reed, a fisheries biologist with the National Marine Fisheries Service, said the recent bump probably is due to multiple reasons - the wet spring in 2010, in increase in early arriving salmon last year, increased flows on rivers like the Stanislaus overall and even natural cycles.

Reed also said biologists get "very concerned" when there are a number of successive years when the populations drop, making the recent numbers promising for the fish and the waterways.

"They do require cold, clear water for their survival, and they're not really durable with crummy water quality conditions," she said.

Demko said pinpointing reasons for the recent changes isn't easy. Because the recent increases are being seen in the whole system, Demko said the cause lies somewhere either downstream in the Delta or, more likely, improved conditions in the ocean.

And researchers are seeing more hatchery salmon raised elsewhere and released in the San Francisco Bay by public agencies spawning in the Stanislaus. That could be problematic, since hatchery fish could degrade the genetic strength of the native salmon.

"The population is trending up, but underlying management issues haven't been resolved yet," he said.

And while experts say more salmon can mean an improved waterway, Reed pointed out there's value outside of the water as well.

"There is something just charismatic about salmon," she said. "When you're standing on the bridge in Knights Ferry in November and watching them do their thing, it's pretty amazing."