Urban tropical estuaries are susceptible to the increased magnitude of precipitation events due to climate change. Resultant floodings, in combination with faulty wastewater infrastructure, exposes urban coastal communities to contaminated surface waters. Such is the case of the Caño Martín Peña (CMP) in Puerto Rico. This is one of the main channels in the San Juan Bay Estuary (SJBE), located in the northeast region of the island. The SJBE is habitat to diverse flora and fauna, and consists of interconnected lagoons, bays, and canals where freshwater and saltwater meet. The CMP stands out for its infilling history which has caused decreased waterflow and persistent flooding of adjacent streets, schools, and homes. The CMP coastal communities are vulnerable to sewage enriched floodwaters due to the lack of appropriate sanitary and stormwater infrastructure. To assess exposure risk, monthly water samplings have been conducted since 2021 at 16 sites throughout the SJBE. We quantified fecal indicator bacteria (FIB) using the defined substrate method and quantitative PCR assays. Data demonstrated that the CMP exceeds acceptable limits for Enteroccocus (35 CFU/100 ml) and E. coli (200 CFU/100 ml) 100% of the time, while other SJBE sites exceeded the criteria levels for Enterococcus and E. coli only 46% and 31% of the time, respectively. We also explore the relationships of environmental parameters such as precipitation, turbidity, dissolved oxygen, pH and dry/wet seasons on FIB concentrations to establish the natural variability of an urban estuarine ecosystem versus the influence of watershed stressors on microbial water quality. Our results emphasize the need for environmental restoration in many regions of the SJBE and the urgency of informing the public to reduce their health exposure to polluted recreational waters, especially in the CMP communities.