It suggests a variety of causes, ranging from global warming to the invasion of the zebra mussel. But it also points a finger at five power plants that take in river water - and millions of fish and fish eggs each year - to cool their equipment.
"Even if the power companies are not the sole cause of degradation of the Hudson River fish community, the loss of such high proportions of the fish populations must be important," the report says.
The environmental group Riverkeeper, which commissioned the study from Pisces Conservation Ltd., a British consultant, released the study at a riverside news conference Thursday morning.
Riverkeeper has been trying for years to force power plants to upgrade their cooling systems to a closed-cycle type that would use 97 percent less river water. The group's president, Alex Matthiessen, said Wednesday that the Clean Water Act requires that such technology be updated and that he would call on the state Department of Environmental Conservation to enforce the requirement.
"Power plants have been slaughtering billions of fish each year," he said Thursday. "You have to try and address all the factors that are playing a role, and at the very least, you have to make sure that the various parties responsible are following the law."
Matthiessen said the study's findings surprised him.
"We've managed to improve the river over the last four decades. We thought it would only make sense that as the river became cleaner the ecosystem upon which the fish depend would become healthier," he said.
The biggest fish intake is at the Indian Point nuclear power plants in Buchanan. Jim Steets, a spokesman for plant owner Entergy Nuclear, disputed the study's findings.
"The Hudson River's fish population is healthy and abundant, and we've seen no connection between the operation of these plants and the adult fish population," he said.
Steets noted that environmental lawyer Robert F. Kennedy said in 2006 that the Hudson has more fish per acre than any other river in the country.
Steets said that by using screens, Indian Point safely returns most adult fish to the river. Most fish eggs are fated to die anyway, he said.
It's been known for some time that some Hudson species were not faring well. Overfishing and dam construction have been devastating the American shad for decades, and an annual shad festival on the Hudson was held without any shad on the menu this year.
But the cumulative nature of the new report - which analyzes several surveys of young fish populations conducted by power companies as a requirement of their licenses - is important, said Andy Kahnle of the DEC's Hudson River Fisheries unit.
"There's lots of different sampling techniques and different ways to interpret the data, but it's good to look into what's happening to some of the fish we don't hear a lot about," he said. "The findings change year to year, but certain species are definitely in decline."
Kahnle noted that several of the species, while down from their 1970s numbers, are up over the last several years. These include white perch, tomcod and bay anchovy. But the reasons for such increases aren't any better known than the reasons for the longer-term decreases, he said.
Kahnle also said some of the findings "have to be taken with a grain of salt."
Sampling the white perch population, for example, is difficult, as the species spends much of its life in weed beds, he said.
The other species reported in decline are the alewife, hogchoker, white catfish, weakfish and blueback herring.
The striped bass, bluefish and spottail shiner have increased their numbers, the study says.
The report found that the river's temperature, measured at Poughkeepsie, had risen 3.6 degrees since the 1960s, and some of the declining species are not tolerant of the higher temperatures, which help decrease dissolved oxygen in the water.
"Given the considerable efforts that have been taken to reduce organic pollution, and the great improvement in water quality in the vicinity of New York City, these declines in DO are disappointing," the report says.
Besides the 13 species studied, Matthiessen said several other Hudson residents are in trouble, including the American eel, the sturgeon and the smallmouth and largemouth bass.
