Sediment has been identified as a significant threat to water quality and channel clogging that in turn may lead to river flooding. With the increasing awareness of the impairment from sediment to water bodies in a watershed, identifying the locations of the major sediment sources and reducing the sediment through management practices will be important for an effective watershed management. The annualized agricultural non-point source pollution (AnnAGNPS) model and newly developed GIS interface for it were applied in a small agricultural watershed, Redrock Creek watershed, Kansas, in this pilot study for exploring the effectiveness of using this model as a management tool. The calibrated model appropriately simulated monthly runoff and sediment yield through the practices in this study and potentially suggested the ways of sediment reduction through evaluating the changes of land use and field operation in the model for the purpose of watershed management.