Hydrologic models are increasingly used to support decisions at various levels and guide water resources policy formulation, management and regulations. In this study the Soil and Water Assessment Tool (SWAT) was examined for its applicability in wetland catchment of Rugezi in Rwanda covering an area of, approximately to, 197 Km2 . The study adopted SWAT model as recommended by others workers in the region in order to extend its testing. The application of SWAT model entailed setting up the model using readily available data, sensitivity analysis and calibration. In this study wetland model physical parameters such as width, depth, length, slope and area were generated by GIS based SWAT interface. The ground photos available from literature supplemented and validated the GIS data. An independent simulation was also conducted without implementing the wetlands in order to study its impacts on the hydrology. Sensitivity analysis indicated that Channel effective hydraulic conductivity (CH_K2), Surface runoff lag time (Surlag), SCS runoff curve number under moderate moisture condition (CN2), and Manning’s n value for main channel (Ch_n) are the most sensitive parameters. Comparable results between simulated and observed streamflows at the catchment outlet, Rusumo gauging station, were obtained. The Nash and Sutcliffe coefficient values (CE) and Index of Volumetric Fit (IVF) were 49.15% and 95.6% for calibration and 51.4% and 98.6% for validation periods, respectively, indicating a satisfactory simulation. It was evident from this study that the wetland was a major hydrological controlling feature in the basin and should be safeguarded. These results suggest that SWAT model is potentially useful in studying the hydrology of natural wetland catchments with limited data. Besides, the authors would like to recommend extensive testing of the model in other wetland catchments in the region.