The New England Fishery Management Council voted Thursday to limit the number of river herring and shad incidentally caught by trawlers in federal waters. The cap is the latest in a series of state and federal measures underway to protect the species of fish, whose populations are at historic lows.

Under the new rules, fishermen trawling for Atlantic herring in southern New England waters would be barred from keeping more than 212 metric tons of river herring and shad bycatch. The cap for the Gulf of Maine would be 86 metric tons.

Caps would not apply to smaller scale vessels, and no caps are proposed in the Georges Bank area where officials say fishermen rarely catch river herring and shad.

River herring spend most of their lives in the ocean but run up freshwater streams and ponds to spawn. They were once a significant resource harvested in Vineyard waters in the spring. The roe was highly prized, sold often at local fish markets. Fishermen also would use the herring as bait to catch lobsters or larger sport fish like striped bass.

Over the years river herring populations have declined due to overfishing and habitat loss. In 2006, Massachusetts implemented the first of several three-year moratoriums on catching river herring in state waters. Other states, including Connecticut, Rhode Island and even North Carolina followed suit. Hundreds of millions of dollars were spent to remove dams and restore the river herring’s habitat. On the Island, there are several fish ladders to aid the fish in spawning.

As protection measures took hold, some in the sports fishing community maintained that the decreased stocks were related to accidental harvesting offshore rather than local consumption.

On Friday, one such local fishermen expressed approval of the Fishery Management Council’s new recommendations.

“It’s about time,” said Buddy Vanderhoop, a member of the Wampanoag tribe who previously ran the tribe’s herring run in Aquinnah.

“They have hurt all the river herring throughout New England,” he said. “We’ve had a moratorium for years and those guys have been able to get away with murder.”

Pat Fiorelli, a spokesman for the New England Fishery Management Council, said council members expressed little opposition when discussing the recommendations, which were first proposed three years ago. “People are aware there is a problem and this one of the actions being taken,” she said.

The recommendations must be approved by the National Marine Fisheries Service. If approved, they are expected to take effect in 2014 and 2015.