In this study, ten best management practices (BMP) were implemented on agricultural areas in the Saginaw River Watershed using the Soil and Water Assessment Tool model based on four targeting methods (Load per Subbasin Area Index (LPSAI), Load per Unit Area Index (LPUAI), Concentration Impact Index (CII), and Load Impact Index (LII)). The effective BMPs both for targeting and non-targeting pollutants were contour farming (CF) (except total nitrogen reduction during total phosphorus targeting scenario), residue management 1000 kg/ha and 2000 kg/ha, strip cropping, recharge structures, terracing, and native grass (NG). In contrast, conservation tillage and no tillage did not reduce significant amount of pollutants for any combination of targeting methods and priority areas. In regard to spatial correlation between targeting methods, a strong relationship was found between the LPSAI and LPUAI methods both for the sediment and total nitrogen targeting scenarios. In addition, a similar result was found between the CII and LPSAI targeting methods. Regarding the spatiotemporal variability of BMP implementation plan, distinct change in priority area was observed in the case of NG implementation by the end of the second year; however, this impact was minimal for CF due to less pollutant reduction efficiency compared to NG. Copyright © 2012 John Wiley & Sons, Ltd.