At many public beaches, routine monitoring of beach water quality using fecal indicator bacteria is conducted to evaluate the risk of recreational water illness. Results from water sample analysis can take over 24-hr, which may no longer accurately reflect current water quality conditions. This study aimed to assess which combination of environmental factors best predicts fecal contamination (E. coli) levels at two of the most popular beaches on Lake Winnipeg, Manitoba (Gimli and Grand Beach), by linking water quality data and publicly available environmental data from 2007 to 2021. We developed separate mixed effects models for each beach for two outcomes, linear (continuous log-transformed E. coli concentration) and categorical (200 CFU/100 ml threshold), to explore differences in the predictors of E. coli concentrations and exceedances of the provincial health risk threshold, respectively. We used a Directed Acyclic Graph to choose which predictor variables to include in the models. For both beaches, we identified clustering of the E. coli outcomes by year, suggesting year-specific variation. We also determined that extreme weather days, with higher levels of rainfall in the preceding 48-hr, previous day average air temperature, and previous day E. coli concentration could result in a higher probability of E. coli threshold exceedances or higher concentrations in the water bodies. In Grand Beach, we identified that days with lower average UV levels in the previous 24-hr and antecedent dry days could result in a higher probability of E. coli threshold exceedances or higher concentrations. The findings can inform possible trends in other freshwater settings and be used to help develop real-time recreational water quality predictive models to allow more accurate beach management decisions and warrant enhancement of beach monitoring programs for extreme weather events as part of the climate change preparedness efforts.