In the last couple of years, different hydrological research projects were undertaken in the Migina catchment (243.2 km2), a tributary of the Kagera river in Southern Rwanda. These projects were aimed to understand hydrological processes of the catchment using analytical and experimental approaches and to build a pilot case whose experience can be extended to other catchments in Rwanda. In the present study, we developed a hydrological model of the catchment, which can be used to inform water resources planning and decision making. The semi-distributed hydrological model HEC-HMS (version 3.5) was used with its soil moisture accounting, unit hydrograph, liner reservoir (for base flow) and Muskingum-Cunge (river routing) methods. We used rainfall data from 12 stations and streamflow data from 5 stations, which were collected as part of this study over a period of two years (May 2009 and June 2011). The catchment was divided into five sub-catchments each represented by one of the five observed streamflow gauges. The model parameters were calibrated separately for each sub-catchment using the observed streamflow data. Calibration results obtained were found acceptable at four stations with a Nash–Sutcliffe Model Efficiency of 0.65 on daily runoff at the catchment outlet. Due to the lack of sufficient and reliable data for longer periods, a model validation (split sample test) was not undertaken. However, we used results from tracer based hydrograph separation from a previous study to compare our model results in terms of the runoff components. It was shown that the model performed well in simulating the total flow volume, peak flow and timing as well as the portion of direct runoff and base flow. We observed considerable disparities in the parameters (e.g. groundwater storage) and runoff components across the five sub-catchments, that provided insights into the different hydrological processes at sub-catchment scale. We conclude that such disparities justify the need to consider catchment subdivisions, if such parameters and components of the water cycle are to form the base for decision making in water resources planning in the Migina catchment.