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The Ethiopian rift is known for its diverse landscape, ranging from arid and semi-arid savannahs to high and humid mountainous regions. Lacustrine sediments and paleo-shorelines indicate water availability fluctuated dramatically from deep fresh water lakes, to shallow highly alkaline lakes, to completely desiccated lakes. To investigate the role lakes have played through time as readily available water sources to humans, an enhanced knowledge of the pace, character and magnitude of these changes is essential. Hydro-balance models are used to calculate paleo-precipitation rates and the potential pace of lake level changes. However, previous models did not consider changes in hydrological connectivity during humid periods in the rift system, which may have led to an overestimation of paleo-precipitation rates. Here we present a comprehensive hydro-balance modeling approach that simulates multiple rift lakes from the southern Ethiopian Rift (lakes Abaya, Chamo, and paleo-lake Chew Bahir) simultaneously, considering their temporal hydrological connectivity during high stands of the African Humid Period (AHP, ~15–5 ka). We further used the Surface Energy Balance Algorithm for Land (SEBAL) to calculate the evaporation of paleo-lake Chew Bahir's catchment. We also considered the possibility of an additional rainy season during the AHP as previously suggested by numerous studies. The results suggest that an increase in precipitation of 20–30% throughout the southern Ethiopian Rift is necessary to fill paleo-lake Chew Bahir to its overflow level. Furthermore, it was demonstrated that paleo-lake Chew Bahir was highly dependent on the water supply from the upper lakes Abaya and Chamo and dries out within ~40 years if the hydrological connection is cut off and the precipitation amount decreases to present day conditions. Several of such rapid lake level fluctuations, from a freshwater to a saline lake, might have occurred during the termination of the AHP, when humid conditions were less stable. Fast changes in fresh water availability requires high adaptability for humans living in the area and might have exerted severe environmental stress on humans in a sub-generational timescale.