Faecal contamination often enters drinking water sources through emergency discharges, which occur as a result of technical malfunctions or a hydraulic overload of the sewer system during periods of heavy rain. In October–November 2012, several emergency discharges entered Lake Rådasjön – a drinking water source for Gothenburg, Sweden. To describe and forecast the influence of these emergency discharges on the microbial water quality, the spread of Escherichia coli (E. coli) within the lake was simulated using a three-dimensional hydrodynamic model. The model was run for a period of 4 months using the observed data, and for a period of 9 days using meteorological forecast data. The modelling results showed how much every contamination source contributed to the total E. coli concentrations at the water intakes. The agreement between the modelling results and the measured concentrations was satisfactory. The results of this study led to the decision to use the lake for drinking water production. This study demonstrated that the proposed modelling approach can be used to provide short-term forecasts of the microbial water quality in drinking water sources.