Microbial contamination of surface waters constitutes a health risk for drinking water consumers which may be lowered by closing the raw water intake. We have evaluated microbial discharge events reported in the river Göta älv, which is used for raw water supply to the city of Göteborg. Elevated levels of faecal indicator bacteria were observed during periods of closed raw water intake. High bacteria levels were, however, also occasionally detected during periods of open intake, probably as a result of microbial discharge far upstream in the river which may be difficult to predict and manage by closing the intake. Accumulated upstream precipitations, resulting in surface runoff and wastewater contaminations in the catchment, correlated positively with the levels of total coliforms, E. coli, intestinal enterococci and sulfite-reducing clostridia. Levels of faecal indicator organisms were negatively correlated to the water temperature due to enhanced survival at lower temperatures. Wastewater discharges from a municipality located just upstream of the water intake resulted in elevated E. coli concentrations downstream at the raw water intake for Göteborg. To improve the prediction of microbial contaminations within the river Göta älv, monitoring data on turbidity and upstream precipitation are of particular importance.