The San Joaquin River Group Authority filed the suit on Thursday in federal district court in Fresno.

It argues that the National Marine Fisheries Service and its related agencies violated their duty to protect the threatened Sacramento River fall run of Chinook salmon by allowing a full commercial season.

If the fish continue recent population declines and become a federally endangered species, the authority's members would be forced to release more of their water to increase river flows, said Allen Short, the authority's coordinator who is also general manager of the Modesto Irrigation District.

"The potential that additional water would have to be released to address dangers for endangered salmon could have a negative impact to our agriculture and industrial customers," Short said.

The authority is comprised of irrigation districts in Modesto, Merced, Turlock, Oakdale and the South San Joaquin Irrigation District, among others. San Francisco is also a member of the authority.

After predictions of a more robust salmon return this year, commercial fishermen on May 1 opened the first full-length season since 2007. Cancelled seasons in 2008 and 2009 and a shortened season in 2010 left many fishermen struggling to make a living.

But federal fisheries managers estimated 730,000 Chinook would return to the Sacramento River this fall. This run of salmon provides many of the fish caught off California and southern Oregon, and has been plummeting in numbers in recent years.

The lawsuit filed Thursday is just the latest salvo in the battle between fishing and agriculture interests over the reasons behind the precipitous declines of fall run Chinook salmon in recent years.

The rebound that accounted for this year's commercial season is in part because of improved ocean conditions, each side agrees.

But in 2008, a federal court imposed restrictions on the huge delta pumps that move water to farms and cities while litigation over the fate of the salmon and the tiny Delta smelt was heard.

These restrictions, which allowed more water to flow in the Sacramento and San Joaquin Rivers, give the fish a better chance of surviving the swim through the delta and out through the Golden Gate to the Pacific Ocean. Some believe this year's expected rebound is not just a coincidence, and the improved flows are working.

Zeke Grader, president of the Pacific Coast Federation of Fishermen's Association, a commercial fishing industry group, said the idea that fishing is a threat to the overall health of the salmon fishery is misguided.

The winter and spring runs of Chinook salmon are already on the endangered species list and are not impacted by commercial fishing, he said.