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The discharge of fecal indicator bacteria into surface water sources poses treatment challenges to drinking water utilities. Changes in the discharge regimes of streams resulting from extreme precipitation associated with climate change can exacerbate these challenges. The catchments of many surface water sources depended upon by water treatment plants are ungauged, thus making it difficult to predict the impacts of climate change on the microbial quality of such water sources. In this study, a hydrological model is implemented to assess the impact of local climate projections on flow regimes and E. coli discharge in the ungauged catchment of the drinking water source for the city of Alesund in Norway. We performed separate sensitivity analysis for flow and E. colt, and assessed the variations in patterns of flow and E. coli concentrations in the streams in future using adjusted meteorological data. The calibrated flow showed good agreement with the observed data, but the E. coli model yielded lower performance indices. The results indicate that interception of precipitation by forest cover and soil organic carbon content mostly control flow generation in the catchments, and the variations in the concentrations of E. coli were more sensitive to instream sediment processes. Flow levels in the streams would remain the same in 2045 and 2075. Peak flows that currently occur in spring and autumn months may respectively shift back to winter and summer months. High concentrations of E. coli currently observed in summer in the streams may be lower in future, but the concentrations may be high at the start of autumn seasons. The results have management implications for watersheds and water utilities mostly in temperate climate regions.