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The SWAT2009 (Soil and Water Assessment Tool, version 2009) model was implemented for prioritizing 12-digit hydrologic unit code (HUC) subwatersheds based on average annual flow-weighted concentration of sediment, total phosphorus (TP), and nitrate-nitrogen (NO3-N) within the Arkansas part of Illinois River Drainage Area (IRDA). The model was set up to simulate change in land use and land cover conditions during 1992 to 2006 by using six remote sensing images for the years 1992, 1993, 1999, 2001, 2004, and 2006. The key model parameters for adjustment were identified by performing sensitivity analysis using a combination of Latin-Hypercube (LH) and one-factor-at-a-time (OAT) sampling methods. The model was calibrated for flow, sediment, TP, and nitrate-nitrogen outputs by optimizing parameter values at hydrologically disconnected gages using a multiobjective function. The multiobjective function consisted of percent relative error (RE), Nash-Sutcliffe efficiency (NSE), percent bias (PBIAS), and ratio of the root mean square error to the standard deviation of measured data (RSR). This function was also used for validating the model at spatially distributed nested gages in the watershed. The output of the validated model was used for identifying priority subwatersheds that can potentially be used for making appropriate decisions for mitigating pollution sources by planners and other interested stakeholders.