The model simulation focuses on an extreme rainfall event that triggered a flood hazard in the Lake Victoria basin region of East Africa from June 24th to 26th, 2022. This study investigates the impacts of its urban canopy on the extreme rainfall events over the Lake Victoria basin in East Africa, employing the Weather Research and Forecasting (WRF) model at a convective-permitting resolution. The rapid urbanization of the region has given rise to an urban canopy, which has notable effects on local weather patterns, including the intensity and distribution of rainfall. The model incorporates high-resolution land use and urban canopy parameters to accurately capture the influences of urbanization on local weather patterns. This research comprises three sets of experiments, two with urban areas and one without, using the WRF model; the experiments focus on three days of an extreme rainfall event in the Lake Victoria basin. Satellite-based precipitation products and reanalysis datasets are employed for a synoptic analysis and model evaluation. The results demonstrate the model’s effectiveness in capturing meteorological variables during an extreme event compared to observed data. The synoptic patterns reveal that, during the extreme event, the Mascarene and St. Helena influenced rainfall conditions over the Lake Victoria Basin by directing moist air toward the northwest. This led to increased moisture convergence from the urban–rural interface toward urban areas, enhancing convection and processes that result in extreme rainfall. Moreover, this study indicates that the urban canopy, specifically the building effect parameterization, significantly amplifies the intensity and duration of rainfall in the urban areas of the region. This research also indicates a general increase in air temperature, relative humidity, latent heat flux, and surface sensible heat flux due to the urban canopy. These findings highlight the substantial influence of urbanization on rainfall patterns in the urban environment.