The Soil and Water Assessment Tool (SWAT) was used to simulate stream flow and predict the impact of different agricultural management practices on atrazine concentrations in the Cedar Creek Experimental Watershed (CCEW) within the St. Joseph River Basin in northeastern Indiana. The model calibration and validation procedures consisted of five and two year periods, respectively. The National Agricultural Statistics Service land use classification (NASS 2001) and the Soil Survey Geographic Database (SSURGO) were used as model input data layers. Data from the St. Joseph River Watershed Initiative, and the Soil and Water Conservation Districts of Dekalb county, were used to represent agricultural practices in the watershed, which included the type of crops grown, different tillage practices, and the use of fertilizers and pesticides. Once the model calibration and validation procedures were successfully completed, the model was used to assess the impact of no-till (NT), and spring plowing (SP), as compared to the present conditions (PC) of the watershed, with and without filter strips on the transport of atrazine under corn/soybean cropping systems over a 25-y period. The Nash-Sutcliffe model efficiency (ENS) for both monthly and daily stream flow were 0.66 for the calibration period while for the validation period ENS values were 0.56 and 0.51, respectively. The ENS values for atrazine calibration and validation ranged from 0.43 to 0.59. For the 25-y simulation, the model results showed that the SP tillage practice reduced greater atrazine concentration than the NT as compared to the PC; whereas, all tillage practices in conjunction with filter strips were most effective at reducing long-term atrazine concentrations. Overall, the results of this study indicate that the model was quite effective in simulating and capturing stream flow and atrazine dynamics on a large-scale agricultural watershed.