We have jointly analysed space gravimetry data from the GRACE space mission, satellite altimetry data and precipitation over the East African Great Lakes region, in order to study the spatiotemporal variability of hydrological parameters (total water storage, lake water volume and rainfall). We find that terrestrial water storage (TWS) from GRACE and precipitation display a common mode of variability at interannual time scale, with a minimum in late 2005, followed by a rise in 2006-2007. We argue that this event is due to forcing by the strong 2006 Indian Ocean Dipole (IOD) on East African rainfall. We also show that GRACE TWS is linked to the El Niño-Southern Oscillation cycle. Combination of the altimetry-based lake water volume with TWS from GRACE over the lakes drainage basins allows estimating soil moisture and groundwater volume variations. Comparison with the WGHM hydrological model outputs is performed and discussed.