The Soil Water Assessment Tool (SWAT) was configured for the Puarenga Stream catchment (77 km2), Rotorua, New Zealand. The catchment land use is mostly plantation forest, some of which is spray-irrigated with treated wastewater. A Sequential Uncertainty Fitting (SUFI-2) procedure was used to auto-calibrate unknown parameter values in the SWAT model which was applied to the Puarenga catchment. Discharge, sediment, and nutrient variables were then partitioned into two components (base flow and quick flow) based on hydrograph separation. A manual procedure (one-at a-time sensitivity analysis) was then used to quantify parameter sensitivity for the two hydrologically-separated regimes. Comparison of simulated daily mean discharge, sediment and nutrient concentrations with high-frequency, event-based measurements allowed the error in model predictions to be quantified. This comparison highlighted the potential for model error associated with quick-flow fluxes in flashy lower-order streams to be underestimated compared with low-frequency (e.g. monthly) measurements derived predominantly from base flow measurements. To overcome this problem we advocate the use of high-frequency, event-based monitoring data during calibration and dynamic parameter values with some dependence on discharge regime. This study has important implications for quantifying uncertainty in hydrological models, particularly for studies where model simulations are used to simulate responses of stream discharge and composition to changes in irrigation and land management.