This paper discusses the analysis and modelling of the hydrological system of the basin of the Kara River, a transboundary river in Togo and Benin, as a necessary step towards sustainable water resources management. The methodological approach integrates the use of discharge parameters, flow duration curves and the lumped conceptual model IHACRES. A Sobol sensitivity analysis is performed and the model is calibrated by applying the shuffled complex evolution algorithm. Results show that discharge generation in three nested catchments of the basin is affected by landscape physical characteristics. The IHACRES model adequately simulates the rainfall–runoff dynamics in the basin with a mean modified Nash-Sutcliffe efficiency measure of 0.6. Modelling results indicate that parameters controlling rainfall transformation to effective rainfall are more sensitive than those routing the streamflow. This study provides insights into understanding the catchment’s hydrological system. Nevertheless, further investigations are required to better understand detailed runoff generation processes.