"Our head is in the sand. Ten or 20 years out, it could very well be too late," he said.
He runs an organization called Peconic Baykeeper. He took us to the middle of Quantuck Bay to show us how unhealthy the water really is.
A black and white target that should be visible up to eight feet beneath the surface disappeared after less than one foot.
Brown tide is a bloom of algae that McAllister blames on runoff from underground cesspools. Human waste, McAllister said, turning normally azure blue water into a wasteland.
Now, state officials have placed the entire South Shore estuary on a list of so-called "impaired waterways"
Experts say this brown tide is choking the life out of the ecosystem beneath the surface of this water. So how did we get here? Decades of development, thousands of homes along the South shore and their antiquated cesspools, experts say.
Local authorities have started to address the problem in new homes, like one in Westhampton Beach. Patricia Moreta was forced to build her cesspool above ground, and surround it with a retaining wall that keeps sewage from leaching into the bay.
But for the homes that dot the shore, McAllister says there's almost no regulation to prevent the septic seep.
"Our economy is driven by water use and when this sours on us it'll be a very sad day for Long Island," he said.
The impaired designation means state experts will now study ways to fix the problem. McAllister hopes they can save this resource while they still can.