The "Barneckle," a 35-foot work boat, rolled gently in the murky waters of the Chesapeake Bay, casting a long shadow in the early-morning sun. It was 7 a.m. on a bright August day and Captain Bill Roulette was starting his second run of the day along the 3,000-foot trotline.

On his first try, Roulette had taken only three or four dozen crabs as he steered the boat with one hand and netted the crabs with the other. It takes experience and skill to net the crabs as they come up out of the water on the trotline and Roulette is good at it. But the first run was disappointing and the second catch was even smaller.

"God knows what the hell is causing this," said the 56-year-old Roulette, with a note of despair. "It's very difficult to determine why the crabs bite or don't bite. But that's all we have to go after right now. There's just no rockfish to be found anywhere."

Roulette has been making his living on the bay since 1974, when he gave up a job in a printing plant in Philadelphia and came to Tilghman Island, 20 water miles south of the Bay Bridge, and became a commercial fisherman. He's had good years and bad years, but the trend has been downward. The fish, he says, are steadily disappearing--and like other fishermen he believes some of the blame rests with the amount of chlorine dumped into the bay and its tributaries by 78 sewage treatment plants upstream.

Roulette's feelings are shared by the flotilla of commercial fishermen and the retailers they sell to. They say they are particularly frustrated by the gradual disappearance of aquatic life, especially fin fish, from the bay.

The watermen express concern about the poor availability of rockfish, which is the state fish, gizzard shad, alewives and oysters. The taking of one endangered species, the American shad, was outlawed in 1981.

Once a premier commercial fishing center, Chesapeake Bay is suffering from a diminished reputation. Seafood retailers and restaurants that once depended on the bay now buy elsewhere at higher prices.

Ray Jacobs, who runs a wholesale and retail fish store in Rock Hall, recalled that a short five years ago he was catching 4,000 to 4,500 pounds of rockfish a week. In June of this year, his catch was down to 150 pounds a week.

"The past two summers have been terrible," said Jacobs. "It's not even worth going fishing. Also, the weekend moonlight fishermen take away much of our catch. The price I pay for fish is 300 percent higher that it was three years ago."

Gary Prigi, buyer for O'Donnell's Sea Grille Restaurant in Bethesda, said he has been forced to pay higher prices for out-of-state seafood because of "better quality and more reliability" of delivery. "I purchase oysters from an oyster farm in Long Island because they are cleaner and I can depend on getting them on time."

Prigi said he now pays $40 for a box of 160 oysters. "If I would buy a bushel of oysters from the bay, which have nearly the same amount as a box from Long Island, I'd pay from $18 to $25."

Prigi said prices have "risen considerably every year. But I never know why the prices are raised. If the fishermen don't have much fish, everybody passes the raised prices down the line and it eventually affects the consumer."

Besides the effect of the chlorine, commercial fishermen cite other reasons for the shortage of fish: too many fishermen, inconsistent weather, chemical runoff from farmlands into streams, and lack of eelgrass, which is found in spawning and feeding grounds for anadromous fish in the bay's tributaries.

Anadromous fish are those that spend part of their lives in the sea and move into the freshwater estuaries for spawning and early growth. The chlorine, used to disinfect sewage before it is dumped, is especially harmful to their spawning areas, fishermen claim.

John Gottschalk, president of the board of directors of the Citizens' Program for the Chesapeake Bay, wrote in an article on the effects of chlorine that the chemical is "one of the most challenging environmental problems facing those who are concerned about the bay. The bay contributes to the lives of millions. The great metro area of the upper and lower bay depends directly on bay-related commerce and industry for much of its income."

The problem started, fishermen say, when the Environmental Protection Agency ruled in 1973 that all sewage plants must use chlorine to disinfect their outflow. Although chlorine was later made optional, it has remained in wide use. According to figures from the Tidewater Administration of the Maryland Department of Natural Resources, there has been a sharp decrease in the catch.

In 1975, the catch of rockfish or striped bass was 2.3 million pounds. Only 1.6 million pounds were caught in 1981. During the same period, the alewife catch fell from 585,000 pounds to 68,000 pounds. Gizzard shad fell from 64,424 pounds to 20,000 pounds.

Of the 78 sewage treatment plants in Maryland that deposit chlorine into the bay and its tributaries, six dump at least 100 pounds a day. Two of the six are in the Baltimore area and four are 20 miles or less from Washington. There are five sewage plants along the bay shore.

Pennsylvania plants, which discharge wastes into the Susquehanna River, and Virginia facilities also contribute to the problem in smaller amounts.

Maryland health officials are searching for alternatives to chlorine.

"We are looking into eliminating its use by encouraging alternative methods of treating the effluent," said Mary Jo Garreis, a biologist with the standards, regulations and certifications section of the state's Department of Health and Mental Hygiene.

Alternative methods under study are ozone treatment and ultraviolet radiation. Ozone is an unstable gas that disinfects rapidly when it contacts microorganisms. Ultraviolet light treatment also destroys microorganisms. Both are more expensive than chlorination, Garreis said.

One other method now in use in several plants is dechlorination, the process of adding sulphur dioxide to the effluent to reduce its toxic content.

Larry Simns, president of the Maryland Watermen's Association, acknowleged that the health department has tried to reduce chlorine deposits in the bay.

"We pressured the health department seven years ago to either restrict the amount of chlorine or abolish it, and they have been working to do that," said Simns.

Laboratory studies conducted by the Tidewater Administration indicate that fish eggs have different threshold levels for chlorine. Oyster young can tolerate up to .001 parts per million (ppm) of chlorine. Striped bass can tolerate .07 ppm, and blueback herring can tolerate .3 ppm.

"The level of chlorine deposited depends on the type of treatment in the plant, the characteristics of the stream where the effluent is discharged, and the use of the receiving water, Garreis said. "The level of chlorine ranges from .00 to .5 parts per million."

Chlorine can become more harmful when mixed with other toxic materials already in the water.

The scarcity of rockfish persuaded the watermen to construct 23 ponds in Elkton to provide a freshwater spawning area for them. The operation, sponsored by the Cecil County-Hartford chapter of the Maryland Watermen, is part of the Open Space Program sponsored by DNR.

The ponds, only 10 of which are in use so far, hold around 20,000 fish each. Once the fish are 2 1/2 months old, or two inches long, they are transferred to the bay.

Though most watermen feel this is a step in the right direction, Roulette feels more should be done.

"It's like in the old days when the king killed a messenger who brought bad news," said Roulette, president of the Talbot Chapter of the Izaak Walton League, a conservation group. He has lobbied in Annapolis against chlorination of effluent.

"It didn't change the situation, but at least something was being done. What must be done here is total elimination of chlorine."