Rust tide, a type of algae that can kill finfish and shellfish, is blooming in parts of Shinnecock and Quantuck bays as well as portions of the Peconic Estuary on the East End.

Low levels of the algae, known as Cochlodinium polykrikoides, have been present since July and heavy rains on Aug. 17 fueled an “explosion in cell densities,” according to Chris Gobler, a professor at Stony Brook University’s School of Marine and Atmospheric Sciences.

It was found in concentrations as high as 1,000 cells per milliliter, twice the level at which the organisms can prove deadly to fish and shellfish, he said.

This is the 13th year that the algae has been detected in Long Island waters. It appears in patches and can coat propellers and other equipment a dark red.

“It’s not a solid mass; it’s like clouds floating in the bay,” said Ed Warner Jr., a bayman and president of the Southampton Town trustees.

“I’m keeping my fingers crossed that it’s short-lived and moves on,” he added.

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Cochlodinium polykrikoides is not toxic to humans.

The algae, which are fed by high water temperatures and increased nitrogen levels from runoff and septic systems, can cut off oxygen supply to fish and shellfish, Gobler said.

“It just destroys the functions of the gills,” he said. “The fish end up suffocating.”

Thick blankets of the algae “can literally physically coat bivalves like scallops and gum them up,” Gobler added.

In past years, the rust tide has damaged scallop stocks. It also can drive off bluefish, fluke, snapper and other fish.

“When this stuff rolls in, the fish just roll out,” Gobler said. “The ones that can get away do.”

State Department of Environmental Conservation officials said they have conducted weekly sampling of juvenile fish in Peconic Bay and have not noticed any fish mortalities.

“It is potentially toxic to shellfish and fish, but we haven’t seen anything just yet,” said Karen Chytalo, assistant director of DEC’s Division of Marine Resources.

The agency will continue its sampling and examine data collection to see if conditions change.

Long Island waters annually see several types of harmful algal blooms. Brown tide, which is harmful to shellfish and eelgrass, appeared earlier this year in Great South Bay but dissipated this month.