The brown tide is back.

An overgrowth of the dark-hued algae — harmful to clams and other marine life, but not to humans — has been spotted in the bays from Moriches Inlet to the Shinnecock Inlet on the South Shore in the highest levels seen since 2012, said Chris Gobler, a professor at Stony Brook University’s School of Marine and Atmospheric Sciences.

“There is no other region that has been so vulnerable to these events,” Gobler said in a news release.

Densities of the algae above 50,000 cells per milliliter are harmful to sea life; in this case, the density was found to be more than one million cells per milliliter on Thursday — the highest level found since 2012, Gobler said.

Brown tide was first found on Long Island in 1985.

The outbreak of Aureococcus anophagefferens is “intense and damaging,” the release says. Brown tide blocks out light in the water and is harmful to sea grass. The algae also is harmful to shellfish, keeping them from properly eating and reproducing, according to the New York State Department of Environmental Conservation.

advertisement | advertise on newsday

At this point, brown tide is not blooming in the Great South Bay, which has been affected every other year on average, Gobler said. Still, “that system is being watched carefully,” the release said.

As for cause, there are two factors at play — one that cannot be addressed, and another that can.

That stretch has naturally low levels of tidal flushing, so water doesn’t circulate well, helping to promote the blooms, Gobler said.

Meanwhile, “many septic tanks and cesspools very near the shoreline” are sending nitrogen by way of ground water into the bays, feeding the blooms, according to the release.

Still, this is a “seasonal phenomenon,” Gobler said, as brown tide can’t survive warmer water temperatures, which in those areas are now around the low 70s, he said.