BOSTON – The red tide that shut down shellfish beds from Maine to Buzzards Bay is fading, but scientists are worried that the toxic tide could return to coastal waters as soon as this fall.

The red tide algae drops armored cysts on the ocean floor which act like seeds, bringing the tide back up to 10 years later.

But the cysts can also germinate in just a few months, said Don Anderson, a red tide expert from the Woods Hole Oceanographic Institution on Cape Cod.

“One of the things we’re worried about is that we might see a fall surge of these cells,” he said Thursday.

The toxic algae is absorbed by shellfish, making them unsafe to eat. Officials emphasize that the shellfish on the market are safe, given the extensive safeguards in place.

About half the 1.2 million acres of shellfish beds that Massachusetts shut down beginning in mid-May remained closed on Thursday.

The tide has cost shellfishermen about $2.7 million in lost income, though the number could rise as high as $7 million, Lt. Gov. Kerry Healey said.

This year’s red tide has largely moved out to sea and dispersed, but it takes a while for shellfish that have absorbed the toxic algae to flush themselves clean.

A repeat of a red tide as toxic and persistent as this year’s is unlikely, either this fall or in coming years, because of the unique wind and water conditions that spurred the nearly unprecedented growth of this year’s bloom, Anderson said.

But history suggests the tide will be back for at least the next few years, Anderson said. The only outbreak comparable to this season’s occurred in 1972, and the toxic tide returned to Massachusetts waters over the next two decades, Anderson said.

With the algae cysts now scattered around the ocean floor, the tide could resurface several more times.

“What we see in these events are these, like gypsy moths, … cycles where you may have them every year, but every few years you have a lot,” he said.

Shellfisherman John Grundstrom, 50, of Rowley, remained shut out from clamming Thursday by closures that continued throughout the North Shore. The beds are expected to open in the next week or so, but Grundstrom said he expects more red tide problems over the next few years.

This year, Grundstrom turned to painting, cleaning basements and odd jobs to make up for the lost income.

“This is really starting to wear on me,” he said. “I’d rather be digging clams than playing golf, or going to a Red Sox game, or anything, really. I feel like a turtle out of his shell.”

The bloom of the red tide algae, called Alexandrium, normally moves down from Maine waters to Cape Ann, but can be carried farther south by currents and winds.

This year, strong winds from the Northeast pushed the algae near shore, where it was fed by nutrients carried by unusually high freshwater runoff from this year’s heavy snow and rain.

Some shellfish reached levels of toxicity so high that even a fraction of a meal could have been fatal, Anderson said.

“When we say there are dangerous shellfish, there absolutely were,” he said.

Researchers are working to forecast where red tide will appear next, and how the bloom will move, so shellfishermen and officials can better absorb the effects.

On Wednesday, the National Oceanic and Atmospheric Administration announced a $540,000 grant to Woods Hole Oceanographic Institution for continuing research.

Scientists are also looking into ways to stop the tide altogether, a monumental task that is years away from a solution, Anderson said.