Photo: Steelhead Unlimited: Roy Thomas believes Cal-Am, the water management district and everyone else should be doing a lot more to protect the Carmel River''s ocean-going fish.

Roy Thomas, president of the Carmel River Steelhead Association, wades waist-deep into the Carmel River and shakes a shady tree that''s half submerged-a perfect hiding place for the rare and threatened fish.

"Look under this bush," he says. "See what I''m doing?" he asks, waving the branches. The fish-hole''s vacant.

"In a normal, living river this would be full of healthy, darting fish," he says. The Carmel River is neither normal nor healthy. In fact, if it weren''t for a recent early November rain storm, there would be no water for Thomas to wade in.

This year almost eight miles of the river ran bone-dry. Every summer, the lower river runs dry. There''s no water to carry fish to the ocean. Thousands of steelhead die.

In 1995, the State Water Resources Control Board concluded that too much water is being taken from the Carmel River and that the over-pumping has a harmful effect on the river. The Board ordered the Monterey Peninsula Water Management District to find a new water supply, and California-American Water Company to stop over-pumping. Cal-Am continues to regularly exceed its mandated annual water limit.

"The net result is that fish die," Thomas says.

Thomas and others blame the water company for steelhead deaths. An investigation by the National Marine Fisheries Services (NMFS) may prove Thomas right.

"Due to water withdrawals in the Carmel River, there has been an insufficient flow in the river, which may have caused the death of steelhead, which are listed under the Endangered Species Act," says Amanda Wheeland, a NMFS enforcement attorney. "We are investigating the cause was of the dead steelhead."

While the investigation does not focus solely on the water company, "Cal-Am is one of the largest divertors on the Carmel River," Wheeland says.

Wheeland says NMFS has not decided if it will prosecute Cal-Am for violating the Endangered Species Act.

"No decision will be made until after the case is closed," she says.

Dave Dettman, a senior fisheries biologist who runs the water district''s steelhead recovery facility near the San Clemente Dam, says rescue operations save between 38,000 and 43,000 steelhead a year. He says 10 percent-about 4,000 fish-die because of the over-pumping.

"We have collected dead fish [on the Carmel River] over the past two summers," confirms Dan Torquemada, a NMFS special agent who''s the lead investigator on the case. "That''s about all I can tell you at this point."

Torquemada would not say how many dead fish NMFS collected. Because it is an ongoing investigation, neither Torquemada nor Wheeland would comment further.

Cal-Am Vice President Steven Leonard says he isn''t familiar with the NMFS investigation.

"We have an agreement with the National Marine Fisheries Services about how we take water from the Carmel River and its associated wells," says Leonard, who manages Cal-Am''s Monterey Division. "It''s an agreement to improve the habitat as much as possible for the steelhead. We assume NMFS is monitoring that agreement. And we do work very hard to keep our operation steelhead-friendly. It''s not just for NMFS. It''s good business for us as well."

The fish recovery program works like this: In the spring and summer, when the water level sinks, Dettman and other biologists zap fish with electrical wands, net them, and truck them to a facility downstream from the San Clemente Dam. Here, they raise wild steelhead in pools and a channel, complete with rocks, woody debris and other vegetation that mimics the shoreline habitat.

When water levels rise in the winter, Dettman and crew re-release mature steelhead into the lower river. If the fish are lucky, they''ll make it to the ocean.

Those are the sequences of events in a normal year. This year, however, sediment from the river damaged the pumps that divert water from the river, through the facility.

As a result, no fish were raised in the rescue facility. Instead, fisheries biologists moved the fish further upstream- which is another one of Thomas'' gripes.

"It''s already too crowded upstream," Thomas says. "Rescue is a misnomer. If I took a fish out of here and put it in my goldfish pond, some people would call it a rescue, but that fish is going to die. Dumping them upriver-delayed mortality. That''s what it is."

Dettman says otherwise.

"I wouldn''t go to the extent to say that it''s not healthy for the fish," he says. "The ideal would be to have a stream flowing all the way to the ocean every year." But this never happens. "To compensate, the fish are released upriver or in the facility. We would prefer the facility, but with the facility out of commission, releasing them upriver is better than losing 40,000 fish."

Dettman says he knows Thomas, a regular at water management district meetings. "I''m not going to respond to Roy [Thomas]''s statements," he says. "I consider Roy''s statements sometimes to be exaggerated."

Back on the river, Thomas walks on as the stream narrows and grows shallower. Eventually, it dries up. A wooden post and dozens of impressions of birds'' feet in the dried mud mark the river''s end.

"See these heron feet?" Thomas asks, pointing to the prints. "They''re the ones who do the cleanup. They eat the dead steelhead.

"In the past," he continues. "We [the Steelhead Association] did everything. Since the water management district took over, all we do is complain."

"You can''t run a fish recovery facility like a bureaucracy, with 9-5 work hours," he says. "Sometimes you need to be out there at three, four in the morning. People need water 24-7. Well, so do fish."