The ominous red streaks showed up early this year - patches of rust-colored water as big as an acre spotted this week near the Shinnecock Canal and in Noyack Bay.
East End baymen call it red tide, blooms of harmful algae that can kill captive fish and shellfish. It typically arrives in late August; researchers think this summer's heat wave may have spurred an earlier bloom.
The algae is not harmful to humans, and no large-scale fish kills have been reported since Cochlodinium polykrikoides was first documented in the Peconic Estuary in 2004. But scientists who have witnessed its lethal effects in the lab say it poses a risk to the bay's recovering scallop population.
Stony Brook University researcher Chris Gobler described red tide as a "killing cloud" of tiny organisms that, massed together, slays competing plankton by releasing harmful compounds that burst cell membranes. Lab experiments show similarly fatal effects on larger marine life. "Coming in close proximity to the fish gills, it just tears them apart," Gobler said.
In the wild, fish who can swim away seem to escape unscathed. But outbreaks have wreaked havoc on aquaculture off Korea and Japan because confined fish have nowhere to go.
That's what bayman Ken Mades of Hampton Bays suspects happened to summer flounder he found dead in his nets in Shinnecock Bay last fall. Mades fishes using pound traps - nets suspended from poles in the bay bottom that trap everything from blue claw crabs to butterfish.
"On the north side of the bay where the bloom was heavy, the fluke were dead in the traps," said Mades, 72. "If they could have left, they would have - but they couldn't."
Other Southampton baymen are worried about how the blooms are affecting scallops, only now starting to come back from a crash in the 1980s caused by the onset of a different harmful algal bloom.
Red tide rises to the top of the water column during the day, clumping to create rusty stripes that can stretch several hundred yards. But at night it drops to the bay bottoms, where shellfish cannot escape its reach.
Ed Warner Jr., a Southampton Town trustee and bayman, blames red tide for wiping out a promising set of juvenile scallops he saw two years ago in Noyack Bay. The following November, "we were pulling up dredges and a lot of the shells were just empty," he said. "Only about a half dozen were live."
The blooms don't yet appear to have hurt scallops at a Suffolk-funded restoration project further east, off Orient. There, fast-moving tides sweep the algae quickly past scallop beds, said Chris Smith, a senior educator with Cornell Cooperative Extension of Suffolk County.
But Smith says red tide could jeopardize the species' nascent comeback. "We built the bay scallop back from no landings to over 18,000 pounds of meat," Smith said. "Those landings are worth over $1.3 million to the regional economy."