Environmental conditions influence fecal indicator bacteria (FIB) levels, which are routinely used to characterize recreational water quality. This study examined 15 years of environmental and FIB data at Puntarenas and Jacó beach, Costa Rica. FIB relationships with sea level, wave height, precipitation, direct normal irradiance (DNI), wind, and turbidity were analyzed. Pearson's correlations identified lags between 24 and 96 h among environmental parameters and FIB. Multiple linear regression models composed of environmental parameters explained 24% and 27% of fecal coliforms and enterococci variability in Jacó, respectively. Puntarenas’s models explained 17–26% of fecal coliforms and 12–18% enterococci variability. Precipitation, sea level anomalies, and wave height most frequently explained FIB variability. Hypothesis testing often identified significant differences in precipitation, wave height, daily sea level anomalies, and maximum sea level 24 h prior between days with and without FIB threshold exceedance. Unexpected FIB interactions with DNI, sea level, and turbidity highlight the importance of future investigations. Display omitted •Environmental parameters explained 12 to 27% of FIB geometric mean variability.•Precipitation, sea level anomalies, and wave height most frequently explained FIB variability.•Higher precipitation was associated with exceedance of FIB thresholds.•Greater wave height was associated with exceedance of FIB thresholds.•Greater maximum sea level 24 h prior was associated with exceedance of FIB thresholds.