Abstract. The hydrological system of the Rift Valley Lakes in Ethiopia has recently experienced changes over the past 2 decades. Potential causes for these changes include anthropogenic, hydro-climatic, and geological factors. The main objective of this study was to utilize an integrated methodology to gain a comprehensive understanding of the hydrological systems and potential driving factors within a complex and data-scarce region. To this end, we integrated a hydrologic model, change point analysis, indicators of hydrological alteration (IHA), and a bathymetry survey to investigate hydrological dynamics and potential causes. A hydrologic model (the Soil and Water Assessment Tool Plus, SWAT+) was parameterized for the gauged watersheds and extended to the ungauged watersheds using multi-site regionalization techniques. The SWAT+ model performed very well to satisfactorily for daily streamflow in all watersheds with respect to the objective functions of the Kling–Gupta efficiency (KGE), the Nash–Sutcliffe efficiency (NSE), and percent bias (PBIAS). The findings reveal notable changes in lake inflows and lake levels over the past 2 decades. Lake Chamo experienced an increase in area of 30.1 km2 (9.5 %), an increase in depth of 4.4 m (30.9 %), and an increase in volume of 7.8×108 m3 (27.2 %). In contrast, Lake Abijata witnessed an extraordinary 68 % decrease in area and a depth decrease of 1.6 m (37.2 %). During the impact period, the mean annual rainfall experienced a decrease of 6.5 % and 2.7 % over Lake Abijata and Lake Chamo, respectively. Actual evapotranspiration decreased by 2.9 % in Lake Abijata but increased by up to 4.5 % in Lake Chamo. Surface inflow to Lake Abijata decreased by 12.5 %, while Lake Chamo experienced an 80.5 % increase in surface inflow. Sediment depth in Lake Chamo also increased by 0.6 m (4.2 %). The results highlight that the changing hydrological regime in Lake Chamo is driven by increased surface runoff and sediment intrusion associated with anthropogenic influences. The hydrological regime of Lake Abijata is affected by water abstraction from feeding rivers and lakes for industrial and irrigation purposes. This integrated methodology provides a holistic understanding of complex data-scarce hydrological systems and potential driving factors in the Rift Valley Lakes in Ethiopia, which could have global applicability.