The recovery plan followed a ruling by a federal judge who banned the harvesting of horseshoe crabs from March 15 to June 15 this year on about 25 islands off South Carolina where an estimated two-thirds of the knots stop off during migration.

The consent order also temporarily prohibits a defendant, Charles River Laboratories International, and two other fishing companies, from taking blood from horseshoe crabs for use by the biomedical industry in testing medical products, including vaccines for toxins. The defendants are also barred from holding horseshoe crabs in ponds before being bled — a process that critics say kills some and weakens others.

During this year’s stopover along the shores of the Delaware Bay, all but about 2,000 of the knots counted by Dr. Niles and his team this year were found on the New Jersey side, reflecting the migration-season closing of the state’s beaches where the birds gather, and the repair of dune breaches to prevent horseshoe crabs from being flushed into coastal marshes during high tides, Dr. Niles said. Harvesting horseshoe crabs in New Jersey waters has been banned since 2008 by a state law, whereas a regulated harvest remains in effect in the other bay states including Delaware.

The much smaller number of knots on the Delaware side this year can be mainly attributed to the continued crab harvest there, said Steve Cottrell, president of Delaware Audubon, a conservation group. Even though the harvest of female crabs in the bay remains officially banned by the Atlantic fisheries commission, Mr. Cottrell said a lack of enforcement for quotas had led to suspicions that female crabs were being illegally harvested along with males.

“Delaware’s continuing bait harvest is taking its toll on the horseshoe crab population that uses the Delaware Bay shore for spawning,” Mr. Cottrell said. “Although there may be higher beach disturbance in Delaware compared to New Jersey, closing beaches in Delaware will change nothing if the beaches remain devoid of horseshoe crab eggs during shorebird migration.”

Tina Berger, a spokeswoman for the commission, said it was up to the states to enforce quotas, and that anyone suspecting a violation should notify state officials.