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More than two dozen wooden boards, used to block the normal flow of water, were placed along the Calaveras starting around April 9, Kauffman said. The idea is to conserve water for the upcoming dry season.

Thousands of fish travelling along the channel, however, were trapped when the river went dry. Kevin Melanephy, a foundation worker documenting the length and species of fish caught in the ponds, said most would be left to die when the remaining puddles evaporate during the next week.

"All of these fish are dying," Melanephy said. "No more water is going to come to wash them to the Delta."

It is an annual process that occurs each spring, when the water district installs the boards, called flashboard weirs, said Trevor Kennedy, a project manager for the Fisheries Foundation. More fish seem to have been left behind this year, he said, likely because the wet winter allowed the Calaveras to flow uninterrupted the entire season.

"The river stayed connected pretty much the entire year," Kennedy said.

Some say the water district disregarded the wildlife in the river when it reduced the flows. Bill Jennings, the head of the water watchdog group DeltaKeeper, believes the district violated state code by taking the water levels back too quickly.

Kauffman said the only requirement for reducing flow into channels involves periods where the waters are at flood levels.

The district violated no laws when it installed the flashboard weirs last week, he said.

The workers used a large green net to pull as many fish as possible from the remaining puddles, which were as deep as a foot in some areas and around 20 feet long. They then hunched over the flapping bounty to count and document everything from foot-long carp to tiny catfish and bass.

They also found nearly a dozen small steelhead, the ocean-bound trout known for their silvery skin, and some juvenile salmon. Kennedy said it's important to monitor the number of rare fish that are stranded when the water levels are taken back to prevent the strandings from happening in the future.

"A lot of people don't know this is happening," Kennedy said. "That's why we're out there."

Kauffman said the district and various agencies, such as the state Department of Fish and Game, have worked for years on a habitat conservation plan for the river. Such a plan would likely require the district to install fish screens at New Hogan Dam but allow some rare fish to be killed.