Accurate and punctual precipitation data are fundamental to understanding regional hydrology and are a critical reference point for regional flood control. The aims of this study are to evaluate the performance of three widely used precipitation datasets—CRU TS, ERA5, and NCEP—as potential alternatives for hydrological applications in the Bahr el Ghazal River Basin in South Sudan, Africa. This includes examining the spatial and temporal evolution of regional precipitation using relatively accurate precipitation datasets. The findings indicate that CRU TS is the best precipitation dataset in the Bahr el Ghazal Basin. The spatial and temporal distributions of precipitation from CRU TS reveal that precipitation in the Bahr el Ghazal Basin has a clear wet season, with June–August accounting for half of the annual precipitation and peaking in July and August. The long-term annual total precipitation exhibits a gradual increasing trend from the north to the south, with the southwestern part of the Basin having the largest percentage of wet season precipitation. Notably, the Bahr el Ghazal Basin witnessed a significant precipitation shift in 1967, followed by an increasing trend. Moreover, the spatial and temporal precipitation evolutions reveal an ongoing risk of flooding in the lower part of the Basin; therefore, increased engineering counter-measures might be needed for effective flood prevention.