The temptation to include model parameters and high resolution input data together with the availability of powerful optimization and uncertainty analysis algorithms has significantly enhanced the complexity of hydrologic and water quality modeling. However, the ability to take advantage of sophisticated models is hindered in those models that need a large number of input files, such as the Soil and Water Assessment Tool (SWAT). The process of reading large amount of input files containing spatial and computational units used in SWAT is cumbersome and time-consuming. In this study, the Consolidated SWAT (C-SWAT) was developed to consolidate 13 groups of SWAT input files from subbasin and Hydrologic Response Unit (HRU) levels into a single file for each category. The utility of the consolidated inputs of model is exhibited for auto-calibration of the Little Washita River Basin (611 km2). The results of this study show that the runtime of the SWAT model could be reduced considerably with consolidating input files. The advantage of proposed method was further promoted with application of the optimization method using a parallel computing technique. The concept is transferrable to other models that store input data in hundreds or thousands of files.