In semi-arid regions such as the southwestern zone of Morocco, better management of water resources is crucial due to the frequent flooding phenomena. In this context, the use of hydrological models is becoming increasingly important, specifically in the Aguenza watershed. A multitude of hydrological models are available to make very efficient modeling, and from this perspective, a comparative approach was adopted using two models with different characteristics. Streamflow simulations were carried out continuously at daily time steps using GR4J and ATHYS (2002–2011). The latter was used also to simulate rainfall-runoff events (1984–2014). Simulation results using the distributed model are very efficient compared to those obtained by the lumped model “GR4J”, which shows the disadvantages of neglecting the hydrological processes during a hydrological study. However, a remarkable improvement was observed in the general appearance of the resulting hydrographs and the performance parameters after using the distributed model ((Calibration: NSE, RSR, and PBIAS increased successively by 8%, 6%, and 45.2%); (Validation: NSE, RSR, and PBIAS increased successively by 6%, 4%, and 8.9%)). In terms of flood event simulations, a good concordance between observed and simulated discharge was observed (NSEmedian = 0.7), indicating its great reliability for simulating rainfall-runoff events in semi-arid and data-scarce regions. This research highlights the importance of using hydrological models, specifically the distributed model ATHYS, for the better management of water resources in semi-arid regions with frequent flooding events.