Little is known about how water quality in offshore recreational environments may be impacted by microbes associated with human waste. Point and non-point sources contribute to loading of human enteric viruses to offshore marine waters. In the Florida Keys, the ability of contaminated ground water to reach the offshore reef tract was assessed by sampling surface water, groundwater, and coral mucus along an onshore to offshore transect for fecal indicator bacteria and human enteric viruses. Coral mucus harbored both fecal coliform bacteria and enterococci at levels 10-fold greater than in the corresponding water samples. Results showed that human enteric viruses reached the outer reef tract via contaminated groundwater arising from extensive use of septic systems in the Florida Keys. In densely populated southeast Florida, ocean outfalls and inlets are additional conduits of sewage contamination to the offshore environment. Water, sponge and coral samples were assayed at stations near sewage outfalls, the Port Everglades Inlet, and beaches for presence of human enteric viruses. Noroviruses were detected at high rates in sponges throughout the area but detection in coral and water samples were more prevalent near the Port Everglades Inlet. The high rate of norovirus detection indicates a potential human health threat. Given the common detection of enteric virus nucleic acid in coastal waters, marine mammals (dolphins, Tursiops truncatus) were screened for carriage of similar viruses; dolphin feces were tested for a suite of human-specific and zoonotic pathogens to assess their role as a sentinel species of human health in contaminated waters. Results show that these mammals are exposed to human enteric viruses but the low detection frequency does not indicate primer cross reactivity. The zoonotic bacterium, Campylobacter, was common among surveyed dolphins and indicates a potential threat for both humans and marine mammals. Human enteric pathogens may be ubiquitous in the marine environment, concentrating in sessile organisms (i.e., sponges and corals). Risk assessment studies are needed to determine the weight of these findings for human and ecosystem health. Water column samples alone may underestimate exposure risk.