Hydrokinetic energy system is the process of extracting energy from rivers, canals and others sources to generate small scale electrical energy for decentralized usage. This study investigates the application of soil and water assessment tool (SWAT) in geographical information system (GIS) environment to evaluate the theoretical hydrokinetic energy potentials of selected rivers (Asa, Awun and Oyun) all in Asa watershed, Kwara State, Nigeria. SWAT was interfaced with an open source GIS to predict the flow and other hydrological parameters of the sub-basins. The model was calibrated and validated using observed stream flow data. Calibrated flow results were used in conjunction with other parameters to compute the theoretical hydrokinetic energy potentials of the rivers. Results showed a good correlation between the observed flow and the simulated flow, indicated by Nash-Sutcliffe Efficiency (NSE) and R2 of 0.76 and 0.85 respectively for calibration period, and NSE and R2 of 0.70 and 0.74 respectively for the validation period. Also, it was observed that highest potential of 154.82 MW was obtained along River Awun while the lowest potential of 41.63 MW was obtained along River Asa. The energy potentials obtained could be harnessed and deployed to the communities around the watershed for their energy needs.