Short-term peaks in pathogen concentrations may increase the risks for waterborne diseases considerably. In this study the occurrence of indicator organisms and pathogens in the river Göta älv at the raw water intake to Göteborg was evaluated and related to risk for drinking water consumption. About half of the 24 pathogen samples, taken during event and non-event conditions, were positive for at least one of the following: Cryptosporidium, Giardia, norovirus, enterovirus, Campylobacter and E. coli O157. Positive pathogen detects were often associated with heavy rainfalls and viruses with a sewage emergency discharge. The annualised probability of infection from this type of event was calculated from pathogen concentrations in a QMRA model. Given that the water intake is not closed, the risk given present water treatment seems to be acceptable for Giardia; however, it is at a borderline for Cryptosporidium and insufficient for noro- and enteroviruses. Present results emphasise the need for an appropriate intake regulation with respect to high pathogen loads, as the risk increases with time of exposure to pathogen contaminants. Rather than a threshold level on E. coli, reports on upstream microbial discharges are valuable for quick pathogen indications.