AimsTo identify faecal pollution along the southeastern Florida coast and determine the performance of a reverse transcription-quantitative polymerase chain reaction (RT-qPCR) method for pepper mild mottle virus (PMMoV). Methods and ResultsIn 2014, bimonthly surface water samples were collected from inlets, exposed to runoff and septic seepage, and coastal sites, exposed to ocean outfalls. Analysis of culturable enterococci and a suite of microbial source tracking (MST) markers (BacHum, CowM2, DogBact, HF183, HPyV, PMMoV) revealed faecal pollution, primarily of human origin, at all sites. Since PMMoV was detected more frequently than other MST markers, the process limits of quantification (undiluted to 10(-2) dilution) and detection (10(-2) dilution) for the RT-qPCR method were determined by seeding untreated wastewater into the coastal waters. Simulated quantitative microbial risk assessment, employing human norovirus as a reference pathogen, calculated a 0286 median risk of gastrointestinal illness associated with the PMMoV limit of detection. ConclusionsAll sites met the U.S. EPA recreational water criteria, despite detection of domestic wastewater-associated MST markers. PMMoV correlated only with human-associated MST markers. Significance and Impact of the StudyThis study demonstrated that PMMoV is an important domestic wastewater-associated marker that should be included in the MST toolbox; therefore, future studies should thoroughly investigate the health risks associated with its detection and quantification in environmental waters.