A key control on the response of an urban drainage model is how well the observed rainfall records represent the real rainfall variability. Particularly in urban catchments with fast response flow regimes, the selection of temporal resolution in rainfall data collection is critical. Furthermore, the impact of the rainfall variability on the model response is amplified for water quality estimates, as uncertainty in rainfall intensity affects both the rainfall-runoff and pollutant wash-off sub-models, thus compounding uncertainties. A modelling study was designed to investigate the impact of altering rainfall temporal resolution on the magnitude and behaviour of uncertainties associated with the hydrological modelling compared with water quality modelling. The case study was an 85-ha combined sewer sub-catchment in Bogotá (Colombia). Water quality estimates showed greater sensitivity to the inter-event variability in rainfall hyetograph characteristics than to changes in the rainfall input temporal resolution. Overall, uncertainties from the water quality model were two- to five-fold those of the hydrological model. However, owing to the intrinsic scarcity of observations in urban water quality modelling, total model output uncertainties, especially from the water quality model, were too large to make recommendations for particular model structures or parameter values with respect to rainfall temporal resolution.