One of the most popular areas for fall recreational shellfishing on the Niantic River is closed for the first time in recent memory, after state regulators found an excessive number of boats still docked at marinas in the area.

Area B, the area south of Smith Cove, usually opens for clamming on Nov. 15 and is not open during the summer months.

"It doesn't get clammed all summer, so a lot of people were disappointed to hear it hadn't opened," Jon Hillyer, himself a recreational shellfishermen and owner of Hillyer's Tackle Shop in Waterford, where most of the shellfishing permits for the Niantic River are sold, said Monday. He said it was the first time he remembered that area staying closed on Nov. 15.

Area A, north of Smith Cove, remained open as of this weekend, but that area is open in the summer so the clam beds are "picked over" by this time of the year, he said. An announcement is expected to be made today to close the bed because of Monday's heavy rain.

Another of the region's popular recreational beds, in Stonington, is also closed. The Stonington Shellfish Commission announced Monday that due to heavy rainfall, it has closed Areas A, B, and Outer Quiambaug Cove. These areas will remain closed to the harvesting of clams, oysters and mussels for a minimum of seven days, the commission said.

The Ledge Light Health District announced Monday that shellfish areas E and P in Groton were also closed because of the rain.

The closures in the Niantic River, Groton and Stonington come as some commercial shellfishermen and volunteer members of local shellfish commissions, who oversee recreational beds, have recently been critical of the state aquaculture bureau for taking an overly harsh stance in imposing regulations in the last one to two years.

Patrick Kelly, vice chairman and treasurer of the Waterford-East Lyme Shellfish Commission, said this the first time since 1975, when he began his involvement with recreational shellfishing, that Area B was not able to open on Nov. 15.

"Quite a few people have called us, upset that the area didn't open," Kelly said.

He said it has become increasingly difficult to comply with the aquaculture regulations in recent years.

"These problems will become more disruptive as the (Bureau of Aquaculture's) resources and staff are carrying a much more demanding compliance workload and insufficient budget," he said in an email message.

David Lamoureux Jr., environmental analyst II for the state Bureau of Aquaculture, which regulates commercial and recreational shellfish beds, informed the commission on Thursday that he had surveyed Area B and found about 40 boats in the water at marinas in Area B, and 20 of them still had sanitary facilities installed.

Steve Jensen, spokesman for the state Department of Agriculture, which oversees the Bureau of Aquaculture, said regulations state that Conditional Area shellfishing beds cannot reopen if there are more than 10 boats with sanitation heads moored in there.

He said the aquaculture bureau will continue to survey the area and reopen it to shellfishing when the number of remaining boats falls to the approved number.

Kelly said that in past years, aquaculture bureau staff who surveyed Area B would check with marina owners to determine whether boats were scheduled to be hauled out on or just after the Nov. 15 opening date for Area B.

"Historically, they took time to check with the marinas," he said. "Now they're underfunded, overworked and understaffed."

Hillyer said he understands that the bureau is enforcing the regulations strictly to protect the public.

"It's a safety precaution," he said. "They don't want people to get sick."

In an email message to the commission, Lamoureux said he would check over the next couple of days on whether a sufficient number of boats were out of the water.

j.benson@theday.com

Twitter: @BensonJudy