In Nigeria, particularly in urban areas like Lagos, flooding is a frequent natural hazard. In 2011, Lagos experienced one of its worst floods resulting in significant economic losses and displacement of people. In recent years, Lagos has continued to grapple with flooding challenges, with an equally significant flood episode occurring in 2021. This study focuses on predicting floods and forecasting extremely heavy rainfall in West Africa's equatorial zone using the Weather Research and Forecasting (WRF) model, particularly in humid tropical environments like Lagos. The study discusses the need to review existing flood models and adopt alternative flood models to address the limitations of flood prediction. As potential causes of these rainfall episodes, the interconnections between synoptic systems such as tropical easterly waves, southwesterly winds related to the West African Monsoon, and local topography and oceanic conditions are investigated. Three key metrics: root mean square error (RMSE), mean bias (MB), and mean absolute error (MAE) are used to assess the effectiveness of the computational model. Results indicate that the WRF model, specifically when using the Thompson parameterisation, can estimate the amount of rainfall accumulated over a 24-h period. This suggests that the model can predict the size of daily precipitation during intense rain events. The Thompson scheme shows better performance compared to the WSM6 scheme while evaluating the stations and episodes. During the rainfall episode on July 10, 2011, Thompson's spatial rainfall predictions were better than WSM6, resulting in a decrease in root mean square error (RMSE) of 15–31% depending on the area. Simulations of the July 2021 episode also show better performance, with a decrease in RMSE of 11–25% when comparing Thompson to WSM6 scheme. The Thompson scheme’s improved ability is directly linked to a more accurate depiction of the microphysical mechanisms that control the rainfall formation. By explicitly simulating the dynamics of ice crystals and graupel, it is possible to accurately replicate the processes of orographic lifting and moist convection that are responsible for driving intense monsoon precipitation. In addition, Thompson scheme shows a reduced degree of systemic bias in comparison to WSM6, with a 75% reduction in the average bias in rainfall accumulation over the research area. The combination of the advanced Thompson microphysics method and WRF's atmospheric dynamics shows a high level of accuracy in predicting intense rainfall and the risk of floods in this area with diverse tropical topography.