The Mekerra Basin in northern Algeria is highly vulnerable to severe flood events, such as those in October 1986 and September 1994, which caused significant damage to infrastructure and the environment. To address flood risk, this study applied the Rainfall–Runoff–Inundation (RRI) model to simulate hydrological processes and flood extents. The model was calibrated and validated using discharge data from these historical events. The sensitivity analyses identified hydraulic conductivity, suction head, and channel roughness as key parameters influencing flood peaks. The RRI model demonstrated a strong performance, achieving correlation coefficients of 0.97 and 0.94 for the 1986 and 1994 events, respectively. The model also produced R² values of 0.94 (calibration) and 0.89 (validation), with Percent Bias (PBIAS) values of 0.006 and 0.013, indicating minimal bias. Nash–Sutcliffe Efficiency (NSE) scores of 0.93 (calibration) and 0.86 (validation) confirmed its robustness in simulating event flows. This study represents the first application of the RRI model in the Mekerra Basin and highlights its utility for flood risk assessment in arid and semi-arid regions, offering critical insights for flood management and mitigation strategies.