Wet-weather discharges from urban areas with a combined wastewater system represent a threat for surface waters. In fact, when the system capacity is reached during medium/big rain events, a mixture of stormwater and untreated wastewater is discharged through combined sewer overflows (CSOs) or bypass (BP) of wastewater treatment plants (WWTP). The discharged pollutant loads are highly variable in time and space, making it difficult to correctly monitor and assess the environmental risks for a specific catchment. The present work proposes a methodology to assess the chronic impact of wet-weather discharges from integrated urban wastewater systems (IUWS) by using a stochastic approach. Monitoring data from the literature were used to characterize the discharges and to predict the risk posed by (micro-)pollutants on a yearly basis in an archetype IUWS. Calculated risks from wet-weather discharges are compared against those posed by WWTP effluent. The results show that CSOs pose a higher risk to surface waters compared to WWTP effluent and bypass, with polycyclic aromatic hydrocarbons being the category of micropollutants of major concern for CSOs. Conversely, WWTP effluent discharges are responsible for most of the risk associated with pharmaceuticals. A sensitivity and uncertainty analysis highlighted the importance of performing an accurate estimation of the recipient flow rate, which can provide a better risk estimation than focusing only on the characterization of the discharged concentrations. In climate change scenarios, where recipient flow rate reduction and overflow volume increment is expected, the risk caused by wet-weather discharges may increase for all micropollutant categories, including pharmaceuticals.