Microbial monitoring in marine recreational waterways often overlooks environmental variables associated with pathogen occurrence. This study employs a predictive boosted regression trees (BRT) model to predict Staphylococcus aureus abundance in the Tampa Bay estuary and identify related environmental variables associated with the microbial pathogen’s occurrence. We provide evidence that the BRT model’s adaptability and ability to capture complex interactions among predictors make it invaluable for research on microbial indicator research. Over 18 months, water samples from 7 recreational sites underwent microbial quantitation and S. aureus isolation, followed by genetic validation. BRT analysis of S. aureus occurrence and environmental variables revealed month, precipitation, salinity, site, temperature, and year as relevant predictors. In addition, the BRT model accurately predicted S. aureus occurrence, setting a precedent for pathogen–environment research. The approach described here is novel and informs proactive management strategies and community health initiatives in marine recreational waterways.