Environmental groups working to restore historic runs of marine steelhead trout to Alameda Creek say the rainbows are descended from them. Genetic studies back up their case, they say.

The rainbow trout may serve as breeding stock for restoring steelhead runs. But granting the fish federal protection also could create new regulatory headaches for ranchers and water agencies.

Ranchers -- and the East Bay Regional Park District -- may be forced to take additional steps to keep cows out of streams to protect rainbow trout populations. In addition, water agencies could be forced to release water into streams that they'd rather keep in storage.

A proposal put forward last week by the National Marine Fisheries Service would protect rainbow trout in streams where they're capable of mingling with steelhead trout.

But for now, the rainbow trout behind Calaveras and San Antonio dams are the only landlocked rainbow trout in California proposed for Endangered Species Act protections, said Jeff Miller, director of the Alameda Creek Alliance.

If genetic studies of other landlocked rainbow trout prove those fish are also related to threatened or endangered steelhead, they would be eligible for the same protections, Miller said.

The proposal to protect rainbow trout "is going to get some fierce opposition from agricultural interests and water districts," Miller said.

Volunteers with the Alameda Creek Alliance have taken fin clippings from handfuls of steelhead that still show up at the mouth of Alameda Creek in Fremont. There, the fish are blocked in their attempts to migrate upstream by a concrete structure protecting BART.

But DNA comparisons of those fish are a close match with rainbow trout trapped behind the Calaveras and San Antonio dams.

"It's certainly based on sound science," Miller said of the proposal to extend protections granted to steelhead to the freshwater variant of the species.

"Legally, they're not allowed to list a portion of a species' population. ... It never made sense to conservationists to list ocean-run steelhead, but not their offspring that stay in the streams. It left parts of the population unprotected."

Steelhead trout -- like salmon -- are born in freshwater streams and migrate to the ocean before returning to the streams of their birth to reproduce.

The offspring of some rainbow trout in eastern Alameda County can't reach the ocean because they're trapped in reservoirs behind dams. Dozens of other barriers to fish migration dot Alameda Creek and its tributaries, from its headwaters to the creek's outlet in Fremont.

A task force that includes local water agencies and environmental groups has been working since 1997 to remove those barriers.

The East Bay Regional Park District has removed two small swim dams in the Sunol Regional Wilderness, and the San Francisco Public Utilities Commission plans to take out two dams in Niles Canyon. The Zone 7 water agency in Pleasanton is designing new flood control and water diversion facilities to be fish-friendly.

Miller has lauded those efforts, but said the Alameda Creek Alliance won't hesitate to use protections granted to local rainbow trout to further its goals.

The group has been critical of the East Bay Regional Park District's policy of allowing ranchers to graze cattle on public lands. Miller said protections for rainbow trout may make it more difficult for the park district to justify grazing in the Sunol and Ohlone Wilderness Regional Preserves.

Miller and other environmentalists say cows can harm fish populations by eroding stream banks and trampling spawning beds if they're not kept out of creeks. Steve Bobzien, the park district's ecological services coordinator, said grazing is helping, rather than hurting, protected creatures, including several species of frogs and amphibians.

"There is no data to suggest that livestock grazing is adversely affecting any of these populations, including the rainbow trout," Bobzien said.

Park district biologists maintain that cattle fill a role in the ecosystem once held by wild herds of deer and elk. Cows help prevent the spread of non-native plants and create habitat for ground squirrels, whose burrows provide homes for amphibians such as the California tiger salamander, grazing proponents say.

"Our current land management (practices) ... are very compatible with those populations," Bobzien said. "We've been very proactive in enhancing, protecting and restoring habitat for special-status species."

The populations of some protected amphibians are actually on the upswing, Bobzien said.

Miller said listing rainbow trout under the Endangered Species Act also could have implications for water agencies such as Zone 7 and the San Francisco PUC, which operates the Calaveras and San Antonio reservoirs.

Both agencies are participating in the effort to restore steelhead runs. But Miller said plans to rebuild and possibly expand Calaveras reservoir would have to be carried out without harming rainbow trout populations.

In addition, it may be necessary to change the timing and amount of dam releases to keep streams from drying up or from getting too hot for fish to survive in the summer, Miller said.

The National Marine Fisheries Service is accepting comments on its proposed steelhead and salmon protections until Sept. 13.