Presenting the hydrological research carried out in the Migina catchment (260 km2), Southern Rwanda with the objective to explore the hydrological trends and climate linkages for catchments in Rwanda (26,338 km2), and to contribute to the understanding of dominant hydrological process interactions. Different Hydro-meteorological instrumentations have been installed for several months in the Migina catchment and measurements have been carried out. The trend analysis is based on Mann-Kendall (MK) test and Pettitt test on times series data varying from 30 to 56 years before 2000. The hydrometric data and modern tracer methods is used for hydrograph separation and show that subsurface runoff is dominating the total discharge even during rainy seasons at Cyihene-Kansi and Migina sub-catchments, respectively. Further, a semi-distributed conceptual hydrological model HEC-HMS is applied for assessing the spatio-temporal variation of water resources in the Migina catchment. The model results are compared with tracer based hydrograph separation results in terms of the runoff components. The model performed reasonably well in simulating the total flow volume, peak flow and timing as well as the portion of direct runoff and baseflow.