Runoff and spills have periodically resulted in high levels of fecal coliform and enterococci bacteria in the Florida Keys, resulting in swimming advisories for nearshore waters and beaches.

The most notable bacteria found in the waters around Florida Keys beaches are Enterococci and Vibrio vulnificus. Enterococci are typically used as "indicator organisms" by the Florida Department of Health; their presence in high levels often indicates that the water may be contaminated with fecal matter from stormwater runoff, wildlife, or sewage leaks, leading to temporary swimming advisories. Vibrio vulnificus, however, is a naturally occurring bacterium found in warm, brackish seawater. While rare, it is often referred to as "flesh-eating bacteria" because it can cause severe skin infections and ulcers if it enters an open wound. It can also cause serious illness if contaminated raw shellfish, particularly oysters, are consumed. In 2026, health officials continue to monitor these levels closely, especially after major storms or periods of extreme heat, advising beachgoers with compromised immune systems or open cuts to avoid the water when bacteria counts are elevated to prevent potentially life-threatening infections.