Vibrio bacteria are naturally occurring, but are present in higher concentrations in the summer when the salt water in the Long Island Sound is warmer, and filter-feeding shellfish, like oysters, can concentrate vibrio in their flesh when it's present in the water.

The primary bacterial concerns in Long Island’s coastal waters in 2026 are Enterococcus and Vibrio vulnificus. Enterococcus is a "fecal indicator" bacteria used by the New York State Department of Health to monitor water quality; high levels typically occur after heavy rainfall when "stormwater runoff" carries contaminants from streets and septic systems into the bays and Long Island Sound. This often leads to temporary beach closures to prevent ear, nose, and throat infections or gastrointestinal distress. More severely, Vibrio vulnificus (often sensationally called "flesh-eating bacteria") is a naturally occurring bacterium that thrives in warm, brackish water. While rare, it can enter the body through open wounds or the consumption of raw shellfish. In recent years, warming sea temperatures have seen a slight increase in Vibrio detections further north than in previous decades. Health officials advise swimmers to avoid the water for 24–48 hours after heavy rain and to ensure any open cuts are properly covered with waterproof bandages before entering the ocean or Great South Bay.