Abstract. The US–German GRACE (Gravity Recovery and Climate Experiment, 2002–2017) and GRACE-FO (GRACE Follow-On, since 2018) satellite missions observe terrestrial water storage (TWS) variations. Over 20 years of data allow for investigating interannual variations beyond linear trends and seasonal signals. However, the origin of observed TWS changes cannot be determined solely with GRACE and GRACE-FO observations. This study focuses on the northern part of the East African Rift around the lakes of Turkana, Victoria, and Tanganyika. It aims to characterise and analyse the interannual TWS variations compared to meteorological and geodetic observations of the water storage compartments (surface water, soil moisture, and groundwater). We apply the STL (Seasonal-Trend decomposition using LOESS) method to decompose the signal into a seasonal signal, an interannual signal, and residuals. By clustering the interannual TWS dynamics for the African continent, we define the exact outline of the study region. We observe a TWS decrease until 2006, followed by a steady rise until 2016, and then the most significant TWS gain in Africa in 2019 and 2020. Besides meteorological variability, surface water storage variations in the lakes explain large parts of the TWS decrease before 2006. The storage dynamics of Lake Victoria alone contribute up to 50 % of these TWS changes. On the other hand, the significant TWS increase around 2020 can be attributed to nearly equal rises in groundwater and surface water storage, which coincide with a substantial precipitation surplus. Soil moisture explains most of the seasonal variability but does not influence the interannual variations. As Lake Victoria dominates the surface water storage variations in the region, we further investigate the lake and the downstream Nile River. The Nalubaale Dam regulates Lake Victoria's outflow. Water level observations from satellite altimetry reveal the impact of dam operations on downstream discharge and on TWS decreases in the drought years before 2006. On the other hand, we do not find evidence for an impact of the Nalubaale Dam regulations on the strong TWS increase after 2019.