ISLES OF SHOALS, N.H. – As a fish rancher in a watery pen, Michael Chambers hand-fed 1,200 halibut Friday.

Nine miles out from Portsmouth in a 50-foot University of New Hampshire research boat, Chambers filled a garbage bag with fish pellets, pulled on a wet suit and tank and swam down about 40 feet to a cage where the fish live.

Later, he dove to two other cages, containing about 3,000 haddock each. He climbed in the top and watched while the fish swam around him in a counterclockwise circle.

He surfaced with a grin.

“They stayed calm,” he said from the water. “I think they’re getting used to us.”

Chambers is project manager for UNH’s Open Ocean Aquaculture program, which is doing some of the university’s most important marine research, university officials said.

The university recently celebrated its designation as a top-tier Sea Grant institution, which means it is eligible for hundreds of thousands of dollars in federal grants for marine research and education. UNH is one a handful of institutions with Sea Grant, Land Grant and Space Grant status.

UNH has managed to become one of the most respected marine research institutions in the country despite relatively little direct support from state government. Balancing research, education and outreach is key, said Jonathan Pennock, the director of the university’s marine program.

Last Thursday, university officials brought VIPs, including Rep. Jeb Bradley, out to see one of its most visible marine programs: the Shoals Marine Lab on the Isles of Shoals. The lab, a joint project with Cornell University, is used mostly for teaching students and the public about marine biology.

The fish farm, more than one mile south of the Isles of Shoals, is less visible. Its focus is research more than education.

The research is important because the fish cages are so far from shore. Most aquaculture farms – which supply about a third of the fish eaten worldwide – are in freshwater ponds or protected saltwater bays or fjords.

“I don’t know of any other farm as exposed as ours,” said Chambers, who has been involved with offshore aquaculture in Hawaii and the Gulf of Mexico.

Chambers hopes the UNH project can show that fish such as haddock, halibut and cod can be raised offshore profitably and without harming the environment.

In Maine, aquaculture, primarily salmon farming, is a $75 million-a-year industry. But Maine salmon farmers frequently have run into environmental and legal troubles; in May a federal judge shut down some farms because of environmental problems.

Being offshore might reduce environmental effects. In bays, cages sit on or near the bottom, which can become polluted with food and fish waste. The UNH cages are in more than 100 feet of water; waste is dispersed by strong currents. After about four years of fish farming, albeit on a relatively small scale so far, university researchers say they have yet to measure any changes in mud samples taken beneath the cages.

The water also is clean and at optimal temperature, Chambers said. He believes that will result in faster-growing, better-tasting fish.

No fish have been harvested yet.

On a calm, sunny day like Friday, the challenges of offshore fish farming were hard to imagine. Mosquitoes, an oddity so far away from shore, were the biggest challenge.

But two years ago, Chambers said, a research buoy at the site recorded 50-foot waves. The cages have never been harmed by heavy storms, but getting out to feed fish in winter is impractical. Even in calm water, it’s a challenge.

“Most fish farms have their cages at the surface,” Chambers said. “They can just throw the food out.”

Chambers doesn’t hand-feed the halibut every day. Usually, they are fed from a boat through flexible tubes. The haddock are fed from a yellow buoy that automatically dumps pellets down tubes twice a day. The buoy is self-powered with a windmill and solar panels.

Finding a practical, economical way to feed fish in underwater cages is a key to turning the experiment into a business, Chambers said.

This fall UNH plans to unveil a larger feeding buoy, which will be used to feed 30,000 cod in a new cage. Researchers are working with a Washington state company to develop a 50-foot-tall feeding buoy, complete with living quarters.

Fish farming is seen by some as a cost-effective way to feed the world in the future. University officials said it might be the savior for local commercial fishermen, who increasingly are being kept in dock because of depleted fish stocks.

But Michael Weber, a California research consultant, said raising fish in ocean cages is a poor substitute for rebuilding wild stocks.

Weber wrote a report for SeaWeb, a conservation group, critical of offshore aquaculture. The report said aquaculture could harm wild animals and pollute water.

UNH’s deep-sea plan might reduce the pollution factor, Weber said in a phone interview last week.

But Weber said carnivorous fish such as salmon, cod, haddock and halibut, must be fed more protein than they produce. That and other costs make fish farming profitable only when the fish get a high price. And those prices will increase as wild stocks decline.

“To some extent, the economic success of this kind of aquaculture depends on the decline of wild populations,” Weber said.