It’s 5:30 a.m. and Will Caldwell and his crewman Dave Inoue step into the shallow water to set a seine net at the mouth of the Peconic River, working to prevent another biological and public relations nightmare.

“It’s nothing but fish,” said Caldwell, a Hampton Bays commercial fisherman, of the bait fish swarming the river at sunrise on Wednesday. “They’re everywhere.”

As the net is slowly joined at the ends and cinched, the fish rise to the surface and gather into a shimmering, flapping mass.

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They’re pulled to the boat and scooped into 100-pound plastic totes using a large brailer with an electric winch and a shovel. In an hour and a half, two tons of fish are in the boat. The two men plan to take 20,000 pounds by noon.

Caldwell is part of an unprecedented effort to catch and process hundreds of thousands of bait fish known as menhaden before they crowd the river and die en masse as they did last summer, choking beaches and marinas. State, federal and Riverhead Town officials worked this year to push through an emergency measure to increase the local quota for the fish.

State and town subsidies are helping to pay for Caldwell’s catch, which he said has reached upward of 300,000 pounds in the past month, fishing every day.

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“They said, ‘Take what you can handle,’ ” Caldwell said of officials overseeing the effort, which is being conducted with three other commercial fishing boats.

The work is going on not far from where menhaden swarmed the Peconic River and parts of the Peconic Bay this time last year. Officials have blamed the fish kill on a perfect storm of large numbers of fish driven by larger predatory fish, warming temperatures, lower oxygen levels and algae blooms.

“We are going to clear this river out to make sure we don’t have another bunker kill,” said Riverhead Supervisor Sean Walter, who toured the Peconic with Caldwell on Tuesday. “What’s great is they’re capturing the bunker before they get too far up river.”

Earlier this month, the Atlantic States Marine Fisheries Commission’s Atlantic Menhaden Management board approved a measure that allowed local fishermen to take up to 30,000 pounds of bunker a day. That’s up from the normal 6,000 pounds for New York fishermen.

One problem for Caldwell has been that the price of bunker, already low, has crashed to 8 cents a pound as more fish flood the market. For that reason, the Town of Riverhead and the state Department of Environmental Conservation are helping to subsidize the work.

Walter said the town is paying 2 cents per pound of bunker to help make it feasible for fishermen, while the state is contributing another 2 cents. The original budget for the town started at $20,000, Walter said, but he suspects it could blossom to $50,000 by the end of the season.

Walter called the effort “a great example of the DEC working well with fishermen and the town.”

Southampton Town Supervisor Jay Schneiderman said his town board on Thursday will discuss kicking in $7,500 toward the effort. Southampton Town borders the river to the south.

“The idea is that it would be more expensive to clean out the river” after a die-off, Schneiderman said. “Supervisor Walter is convinced that we have already averted a massive fish kill. He may be right.”

Caldwell said he is processing as many fish as he can, though the low price makes margins thin. Last year, after the big die off, the town was offering 30 cents a pound to help scoop all the dead fish from local waters and beaches.

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Lenny Nilson, owner of L&L Wholesale Bait in Bay Shore who has been fishing for bunker on the Peconic for 50 years, said he expects that by the time the season is finished in July, he and the others will have taken 1 million pounds from the water. All local bait shops and wholesalers have their fill of the fish, he noted. Now, most of what they catch goes to Maine for lobster bait.

“We’re a dying breed,” he said.

With Will James