Researchers hoped to find evidence of a healthy new generation of ospreys when they checked 84 nests of the fish-eating bird in mid-June at Mobjack Bay, an inlet at the southern end of the Chesapeake Bay. They found only three young.

It was the lowest reproductive number in more than 50 years of monitoring the local population of the raptor, according to scientists at the College of William & Mary. And they said it represented the latest evidence in a long-term decline in breeding success due to the bay-wide depletion of the bird’s favorite food — Atlantic menhaden.

Hundreds of millions of the little, silvery fish play a crucial role in the ecology of coastal waters all along the Eastern Seaboard, feeding bigger fish like striped bass and weakfish; marine mammals including whales and dolphins; and birds like bald eagles, great blue herons and brown pelicans. The fish are nutrient-rich, a good source of Omega-3 fatty acids; they consume smaller organisms like plankton and they filter huge quantities of ocean water.

But they are also a mainstay of the commercial fishing industry, caught in mass quantities to be processed into bait for crabs and lobsters, and in greater volume for so-called reduction fisheries, in which they are ground up and turned into products including fish oil and fish meal.

This year, the Atlantic States Marine Fisheries Commission, a federal regulator, increased the amount of menhaden allowed to be caught to 233,550 metric tons throughout the Atlantic coast for the next two years, about 20 percent higher than the previous two years. The commission said the new quota would provide additional fishing opportunities while minimizing the risk of damaging the fish’s ecosystem.

The agency concluded last August that there was no evidence that menhaden were being “overfished” across its range, when measured by “ecological reference points,” a network of the fish’s predators and prey that has guided the commission’s menhaden policy since 2020, replacing its practice of management by single species.

While raising the coastwide catch for menhaden, the commission left its quota for the reduction fishery in the Chesapeake Bay unchanged at 51,000 metric tons, or about 244 million fish, based on an average of 0.46 pounds per fish. Across the whole Atlantic coast, the agency authorized a catch of around 1.2 billion fish.

Critics of the commission say the removal of such large quantities of fish from the bay is degrading the ecosystem in which menhaden play a central role, making it harder for species like osprey and striped bass to survive and thrive.

“The Virginia-based menhaden fishery is overfishing the stock of Atlantic menhaden in and around the Chesapeake Bay,” Noah Bressman, a fish biology professor at Salisbury University in Maryland, wrote in a letter to Maryland officials in 2021. “The disappearance of most of the menhaden from the bay is contributing to the disappearance of the many species that rely on menhaden.”

Tina Berger, a spokeswoman for the commission, said there were “numerous factors responsible for declines in other species.” For example, she said, the weakfish population has also been hurt by high levels of predation and disease in recent years.

In May, a group of recreational fishermen from Maryland sued the Virginia Marine Resources Commission, a state agency, claiming it contributed to the decline of menhaden in and around Chesapeake Bay by “rubber stamping” the latest quotas set by the Atlantic commission.

The Southern Maryland Recreational Fishing Organization said that the Virginia agency’s decision was contributing to declining populations of menhaden and other species that depend on them, and that it was harming the recreational fishing industry, which the organization said contributed $1.3 billion a year to the Virginia economy.

The maximum harvest the commission set for Virginia and the Atlantic coast “does not relieve the Virginia commission from the duty to analyze — based on state-specific considerations prescribed by statute — the appropriate maximum harvest in the Virginia portion of the bay, and appropriate conservation measures,” according to the complaint, filed on May 10 in the Circuit Court for the City of Richmond.

Phil Zalesak, a spokesman for the plaintiffs, said the group was seeking a hearing on the matter in September.

The suit accused the state agency of issuing the regulation outside the period set by state law of October through December, and of failing to do its own analysis of the conditions in state waters when adopting the commission’s new quota. It asked the court to invalidate the state agency’s regulation, and to require a new rule that would protect Virginia waters, including the state’s portion of the Chesapeake Bay.

The state agency declined to comment.

Omega Protein, a company based in Reedville, Va., that harvests menhaden for conversion into fish oil and other products, declined to comment on the lawsuit, but endorsed the commission’s argument that menhaden are not overfished. Ben Landry, a spokesman for the company, said that the commission’s current limit on taking menhaden from the Chesapeake Bay was one of the lowest in the 150-year history of the bay’s fishery, and that there was no scientific basis for claims that the fish is locally depleted.

Mr. Landry pointed to striped bass as an example of a fish that was “critically depleted” in the Atlantic waters for reasons other than its food source, attributing the problem to “excessive” recreational fishing that should be curbed by emergency regulations.

“It is clear that the very precautionary Chesapeake Bay cap for menhaden is not the hurdle for the striped bass population returning to higher levels,” he said.

In a statement on its website, the company said the increase in the total allowable catch for menhaden was “fully compatible” with the ecological reference points that underlie the commission’s new management of the fish.

Along the coast since 2015, striped bass had surged in population. But after the recreational catch of striped bass nearly doubled last year over 2021, the Atlantic commission took steps in May to rebuild the population by limiting the maximum size of fish caught by recreational anglers to 31 inches.

Paul Eidman, founder of Menhaden Defenders, a nonprofit that advocates for rebuilding stocks of the species along the Atlantic and Gulf of Mexico coasts, accused Omega of using industrial techniques, including big ships and spotter planes, to catch menhaden in the Chesapeake Bay in numbers that are not sustainable, and that contribute to the decline of other species.

“It’s about the impact that these massive 195-foot vessels have,” Mr. Eidman said in an interview. “They take millions and millions of fish at one time, and it basically strip mines portions of the bay. Game fish and birds and all these other creatures suffer for that. It’s not that the fish aren’t there; it’s that they are getting wiped out too fast for nature to replenish them.”

Mr. Eidman, who also operates fishing charter boats out of Monmouth County, N.J., said Chesapeake Bay was an important source of game fish like striped bass throughout the Atlantic coast. He urged Omega to fish outside the bay so that its stocks of menhaden and other fish can recover from what he and other advocates say is years of overfishing.

“Our contention is: Stay out in the ocean, leave the estuary alone, and be a good steward,” he said. “Omega is always talking about being a member of the community, and always giving back. If they cared so much, they would move their operations out to sea, and leave the estuary alone so it can do its job.”

Outside the Chesapeake Bay, the number of menhaden has increased since the Atlantic commission determined in 2012 that the fish was being harvested at a rate that would exceed its reproductive capacity if not corrected. In response, the agency temporarily cut its total allowable catch by 20 percent coastwide, and the fish population recovered within two years.

Evidence of its recent abundance can be found off the coasts of New York and New Jersey, where more of their predators, including humpback whales, tuna, sharks and bald eagles, have returned, Mr. Eidman said.

At Mobjack Bay, the latest ratio of osprey young raised per nest is only 0.03, sharply lower than the 1.15 rate needed for the population to sustain itself, said Michael Academia, an osprey researcher at the Center for Conservation Biology at the College of William & Mary in Williamsburg, Va.

The record-low level of osprey chicks in the area follows successive declines in the reproductive rate of 1.39 per pair in 1984, 0.91 in 1990 and 0.75 by 2006, all reflecting the local depletion of menhaden stocks, Mr. Academia said.

The Atlantic commission’s assessment that menhaden stocks were not overfished was not accurate for the Chesapeake Bay where the numbers were locally depleted, he said.

Since there are no accurate data on the number of menhaden in the bay, the William & Mary team has used a supplemental feeding program to confirm that birds fed on the fish raise more young than those that do not receive the supplemental fish. Although osprey can feed on other kinds of fish, they much prefer menhaden because the species schools on the surface, and so are easily accessible.

To rebuild the local population of osprey and other creatures that depend on menhaden, the commercial fishing industry, both for bait and reduction fishing, should move out of Mobjack Bay — an important barometer of the osprey population — and from the Chesapeake Bay as a whole, Mr. Academia said. “The menhaden population in Mobjack Bay is not currently adequate to sustain the osprey population,” he said.

The commission’s spokeswoman, Ms. Berger, said the lack of data on menhaden stocks in specific parts of the Atlantic coast limited the agency’s ability to report local data. But she said it hoped to develop more location-specific data in the future.

“The development of models and data that can address finer spatial scales is a research priority for the species,” Ms. Berger wrote in an email. “The current stock assessment (to be completed in 2025) will still evaluate menhaden as a coastwide stock, but it will begin to explore methods and data that could be used in the next assessment to have regional components.”