The objective of this article is to develop and implement a comprehensive computer model that is capable of simulating the surface-water, ground-water, and stream-aquifer interactions on a continuous basis for the Rattlesnake Creek basin in south-central Kansas. The model is to be used as a tool for evaluating long-term water-management strategies. The agriculturally-based watershed model SWAT and the ground-water model MODFLOW with stream-aquifer interaction routines, suitably modified, were linked into a comprehensive basin model known as SWATMOD. The hydrologic response unit concept was implemented to overcome the quasi-lumped nature of SWAT and represent the heterogeneity within each subbasin of the basin model. A graphical user-interface and a decision support system were also developed to evaluate scenarios involving manipulation of water fights and agricultural land uses on stream-aquifer system response. An extensive sensitivity analysis on model parameters was conducted, and model limitations and parameter uncertainties were emphasized. A combination of trial-and-error and inverse modeling techniques were employed to calibrate the model against multiple calibration targets of measured ground-water levels, streamflows, and reported irrigation amounts. The split-sample technique was employed for corroborating the calibrated model. The model was run for a 40 y historical simulation period, and a 40 y prediction period. A number of hypothetical management scenarios involving reductions and variations in withdrawal rates and patterns were simulated. The SWATMOD model was developed as a hydrologically rational low-flow model for analyzing, in a user-friendly manner, the conditions in the basin when there is a shortage of water.