Even as water quality improves in the 153-mile Hudson River estuary, its rich ecosystem is in sharp decline, according to a new report.

The Hudson River Foundation’s “State of the Estuary” report states that temperatures in sections of the waterway stretching from New York Harbor to Troy have risen by as much as 2 degrees Fahrenheit in the last two decades — five times greater than the increase in ocean temperatures per decade.

“The most important finding is really that the estuary waters are warming,” said the report's author, Isabelle Stinnette. “It's very clear it's in almost every water body in the harbor estuary, and then some of the monitoring stations further up the Hudson as well. And it's one of these things that's going to affect a lot of the other indicators, too.”

The report found that rising temperatures are already substantially affecting wildlife. The horseshoe crab population, which the Atlantic States Marine Fisheries Commission assessed as "good" in 2009, was recently downgraded to "poor." Horseshoe crabs at the large spawning ground in Jamaica Bay (while not technically part of the Hudson estuary) had the lowest survival rates of all Atlantic coast populations, according to the report.

“The increase in water temperature that we've already seen has already impacted several species, and continued increase will only affect more species, as well as lead to potential water-quality changes that might make it less hospitable for fish, because the levels of dissolved oxygen won't be high enough in the warmer waters,” said Dan Shapley, senior director of advocacy policy and planning at the nonprofit group Riverkeeper.

The report also found that fish populations were leveling off. More than a half-century ago, commercial catches in the estuary were as much as 100 times what they are now. Disease, bycatch (unintentional capture of species), habitat loss and poor water quality were among the biggest reasons why fish populations were not increasing.

Shapley said Atlantic tomcod and rainbow smelt, which are both cold-water fish, no longer inhabit the estuary. The fish are sometimes found further north in the Hudson River.

“That’s a five-alarm fire,” said Shapley. “We're not seeing recovery in many of our fish species, and they are at very low levels of abundance.”

Aquatic plant life also appears to have plateaued, according to the report. Over the last 30 years, the estuary has lost about half of its submerged aquatic vegetation. Eelgrass, a key species, is no longer found locally. Higher temperatures and water pollution, including sewage, are ongoing threats to aquatic vegetation.

The harm caused by rising temperatures documented in the report contrasts with improvements in the Hudson River estuary’s water quality. The amount of debris removed from the water has been cut in half, from 12 million pounds of debris in 2003 to 6 million pounds in 2023. Nutrients in the water, like phosphorus, nitrogen and dissolved organic carbon, are trending in the right direction, according to the report.

The report shows improvements in the levels of PCBs contamination in fish, an indication that General Electric’s dredging of decades of pollution in the Hudson through the federal Superfund program is making a difference.

The Hudson River is a 315-mile waterway that originates in the Adirondack Mountains, flows through the Hudson Valley and empties into the Atlantic Ocean at New York Harbor. The northern half of the river, above Troy, flows from north to south. The lower half is a tidal estuary connected to the ocean. The river’s mix of ocean and freshwater shifts with tides, creating a diverse ecosystem where bald eagles and other birds feast on more than 200 species of fish, including striped bass.

But that natural bounty is in decline, according to the report. Over the last two decades, sea-level rise and land use have caused the loss of more than 80% of the estuary’s wetlands, about 200 acres. Tidal wetlands absorb floodwaters and mitigate the impact of sea level rise, floods and storm surge. In Jamaica Bay, one of the most significant marsh complexes in the city, the rate of salt marsh loss is calculated to be about 19 acres per year.

“They’re the nursery for everything and a lot of our endangered species exist in these areas,” said Stinnette.