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SWAT (Soil and Water Assessment Tool) is a comprehensive, semi-distributed river basin model that requires a large number of input parameters, which complicates model parameterization and calibration. Several calibration techniques have been developed for SWAT, including manual calibration procedures and automated procedures using the shuffled complex evolution method and other common methods. In addition, SWAT-CUP was recently developed and provides a decision-making framework that incorporates a semi-automated approach (SUFI2) using both manual and automated calibration and incorporating sensitivity and uncertainty analysis. In SWAT-CUP, users can manually adjust parameters and ranges iteratively between autocalibration runs. Parameter sensitivity analysis helps focus the calibration and uncertainty analysis and is used to provide statistics for goodness-of-fit. The user interaction or manual component of the SWAT-CUP calibration forces the user to obtain a better understanding of the overall hydrologic processes (e.g., baseflow ratios, ET, sediment sources and sinks, crop yields, and nutrient balances) and of parameter sensitivity. It is important for future calibration developments to spatially account for hydrologic processes; improve model run time efficiency; include the impact of uncertainty in the conceptual model, model parameters, and measured variables used in calibration; and assist users in checking for model errors. When calibrating a physically based model like SWAT, it is important to remember that all model input parameters must be kept within a realistic uncertainty range and that no automatic procedure can substitute for actual physical knowledge of the watershed.