Fecal indicators and microbial source tracking markers identify shared and site-specific contamination profiles at freshwater and marine beaches.

Conventional recreational water quality monitoring is based on fecal indicator measurements for public health-related water postings or long-term remediation strategies. However, interpretation of recreational water quality is often limited by delayed culture results and the inability of traditional fecal indicators to distinguish contamination sources, which may differ across diverse recreational water environments. To address these limitations, we tested rapid qPCR for enterococci in parallel with tests for microbial source-tracking markers and Escherichia coli culturing at geographically distinct Canadian marine and freshwater beaches. Samples were collected from 10 beaches in Vancouver, Grand Beach Provincial Park, the Niagara region, Halifax, and Toronto during the 2023 to 2025 bathing seasons and analyzed for culture-based E. coli, qPCR-based enterococci, and microbial source-tracking markers. The enterococci qPCR performed well analytically and showed a strong positive association with the same-day retrospective E. coli measure, supporting the operational feasibility of qPCR-based beach monitoring throughout different regions. However, the correlation and agreement in Beach Action Value (BAV) exceedances differed among beaches, suggesting that fecal indicators may not exhibit uniform trends across sites. Source-tracking results revealed that the gull-associated molecular marker (Gull4) was prominent at most beaches and showed consistent positive correlation with fecal indicators overall. The human-associated HF183 marker was prominent only at beaches in larger urban centers. Additionally, Gull4 was the most prevalent marker and showed the strongest and most consistent association with BAV exceedances, whereas HF183 only showed an association with BAV exceedances at one urban beach region. This study demonstrates that rapid molecular monitoring can complement standard culture-based assessment in recreational water monitoring, while MST markers provide source-specific information to support adaptive beach risk management and identify data needs for future Quantitative Microbial Risk Assessment.