Since the beginning of the 2000s, most of the West-African countries, particularly Benin, have experienced an increased frequency of extreme flood events. In this study, we focus on the case of the Ouémé river basin in Benin. To investigate flood events in this basin for early warning, the coupled atmosphere–hydrology model system WRF-Hydro is used, and analyzed for the period 2008–2010. Such a coupled model allows exploration of the contribution of atmospheric components into the flood event, and its ability to simulate and predict accurate streamflow. The potential of WRF-Hydro to correctly simulate streamflow in the Ouémé river basin is assessed by forcing the model with operational analysis datasets from the European Centre for Medium-Range Weather Forecasts (ECMWF). Atmospheric and land surface processes are resolved at a spatial resolution of 5 km. The additional surface and subsurface water flow routing are computed at a resolution of 500 m. Key parameters of the hydrological module of WRF-Hydro are calibrated offline and tested online with the coupled WRF-Hydro. The uncertainty of atmospheric modeling on coupled results is assessed with the stochastic kinetic energy backscatter scheme (SKEBS). WRF-Hydro is able to simulate the discharge in the Ouémé river in offline and fully coupled modes with a Kling–Gupta efficiency (KGE) around 0.70 and 0.76, respectively. In the fully coupled mode, the model captures the flood event that occurred in 2010. A stochastic perturbation ensemble of ten members for three rain seasons shows that the coupled model performance in terms of KGE ranges from 0.14 to 0.79. Additionally, an assessment of the soil moisture has been developed. This ability to realistically reproduce observed discharge in the Ouémé river basin demonstrates the potential of the coupled WRF-Hydro modeling system for future flood forecasting applications.