The pathogen loads within surface waters originating from urban wastewater sources needs to be assessed to support drinking water risk estimations and optimal selection of risk reduction measures. Locally reported discharges from sewer systems (>100,000 persons connected) were used to simulate the potential microbial loads into the Göta älv river, Sweden. Using Monte Carlo simulations, the median and 95% percentile (i.e. worst case) of total microbial load from wastewater treatment plants, sewer network overflows and emergency discharges were assessed and presented for dry and wet weather conditions. Wastewater treatment plants with secondary treatment represented a major source of E. coli, norovirus, Giardia and Cryptosporidium. During wet weather, comparably high microbial loads were found for sewer overflows due to heavy rains. Substantial loads were also associated with an incident of the emergency discharge of untreated wastewater. Simulated river water concentrations of faecal indicators (E. coli, sulfite reducing clostridia, somatic coliphages) and pathogens (norovirus, Giardia, Cryptosporidium) were confirmed by river sampling data, suggesting that urban wastewater is the major microbial source for this river.