In the past four months, one form or another of harmful algae bloom has struck every major bay or estuary in Nassau and Suffolk counties, according to a water-quality assessment released Tuesday by the Long Island Clean Water Partnership.

Chris Gobler, a professor at the Stony Brook School of Marine and Atmospheric Sciences, mapped out cases of rust, brown and blue-green algae outbreaks, and cases of low oxygen in area waters.

The main culprit, Gobler said, is nitrogen pollution fed by antiquated wastewater systems.

“This is really a narrative of what occurred on Long Island from May through today,” Gobler said during a news conference at the Patchogue Ferry Terminal. “In a very short time there was no shortage of impairment of water quality.”

Depending on their type, the blooms can be harmful to shellfish, finfish, eelgrass, small animals and even humans. Beyond being fed by nitrogen pollution, they can also be affected by temperature changes.

“You can draw a line back to overloading of nitrogen for all of these cases,” Gobler said of blooms that appeared from Long Beach to Montauk.

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The recent brown-tide bloom in Great South Bay, which lasted for 10 weeks and can be harmful to shellfish, was the longest and most intense ever documented here.

Hypoxia — a condition where oxygen levels fall below what is sustainable for marine life — was documented in 21 locations, up from five found during a 2013 assessment.

And cases of blue-green algae blooms were documented in 15 lakes and ponds, more than in previous years. That bacteria, which can be fatal to small animals and cause gastrointestinal issues in humans, prompted state officials to warn swimmers away from popular spots, such as Lake Ronkonkoma.

Adrienne Esposito, executive director of Citizens Campaign for the Environment, which is a member of the partnership, said the assessment is necessary to identify water-quality trends and problems in area waters.

Northport for years was home to frequent red-tide blooms, but none have been detected in five years since a wastewater treatment plant was upgraded and storm-water runoff filtered, Esposito said.

“That’s progress,” she said. “So inaction will make it worse but action can make it better.”

Bob DeLuca, president of the Group for the East End, another partnership member, said while the recent blooms may paint a bleak picture, state investment in clean-water programs and Suffolk County’s drive to expand use of advanced septic systems are key to reversing the trend of nitrogen-polluted waters. Efforts like that need to intensify, partnership members said.

“The change we are talking about is finally starting to happen,” DeLuca said.