The availability of freshwater is a particularly important issue in Africa where large portions of the continent are arid or semiarid and climate is highly variable. Sustainable water resource management requires the assessment of hydrological variability in response to nature climate fluctuation. In this study, we used a land surface model – Integrated BIosphere Simulator (IBIS), and a hydrological routing model – Hydrological Routing Algorithm (HYDRA), to investigate the hydrological variability in two large basins, the Lake Chad basin (LCB) and the Niger River basin (NRB), located in West Africa, over the period of 1950-1995. The IBIS land surface hydrological module was calibrated and validated for arid and semiarid Africa; and major enhancements were made to the module, including the development of a dynamic root-water-extraction formulation, the incorporation of a Green-Ampt infiltration parameterization, and modification to the prescribed root distribution, the runoff module and weather generator. The results show that the hydrology in this area is highly variable over time and space. The coefficient of variance (CV) of annual rainfall ranges from 10-15% in the southern portions of the basins to 30-40% in the northern portions. The annual ET varies with a slightly lower CV compared to the rainfall, but the runoff is extremely sensitive to the rainfall fluctuation, particularly in the central portions of the basins (8°N – 13°N in LCB and 12°N – 16°N in NRB) where the CVs in runoff are as high as 100-200%. The annual river discharge varies largely in concert with the rainfall fluctuation, with the CV being 37% in LCB and 23-63% in NRB. In terms of the whole basin, the relative hydrologic variability (rainfall, ET, runoff and river discharge) is significantly higher in the dry period than in the wet period, and the inter-annual variability in runoff is more than twice as high as compared to rainfall or ET.