Bacterial skin infections are a chronic problem among whitewater rafters on the Chattooga River in the southeastern United States; however, little is known about the source of such infections. The Chattooga River is a federally designated "Wild and Scenic" river, with a forested riparian buffer zone designed to protect water quality in the river. Riverine water quality can be negatively impacted by tributaries that are not protected by federal guidelines. Water quality in Stekoa Creek, a major tributary of the Chattooga River, is degraded by sediment that runs off from construction sites near the creek, as well as fecal coliform contamination from wastewater treatment facilities. Degraded water quality may impact the health of visitors recreating on the river, as well as recreation industry workers. We demonstrate that inputs from the impaired creek influence microbial community composition in Chattooga River waters. A survey of whitewater raft guides was conducted to collect data on incidence of skin infection, and to assess perceived health risk from recreation activities. Whitewater rafting guides working on the Chattooga River reported concerns about their personal health related to degraded water quality and microbial contamination from Stekoa Creek. Incidence of bacterial skin infection and perceived health risk was strongly correlated among the whitewater rafting guides (r = 0.67). Concerns about environmental quality appear to be shaped by the incidence of skin infection. Such concerns are also correlated with changes in recreation practices among whitewater rafting guides (r = 0.67).