Morphological study of lakes defines the sensitivity of their watershed. Moreover, it plays important role in safeguarding the lake’s ecosystem services through proper planning and utilization of the lakes’ resources. In the last few decades, the morphology of lakes in Ethiopian and Kenyan Rift (EKR) valley are experiencing contradicting morphological changes. Being in the same system, some are shrinking and others are expanding beyond their natural boundaries. The objective of this review is to shed light on the trends in spatio-temporal water level fluctuation and their contributing factors for lakes to the academia and decision makers. Peer reviewed article journals, conference proceedings, thesis, and book chapters collected from online sources and supplied by authors on request formed a database of 346 documents where 226 are critically assessed. The review indicated that lakes in Ethiopian rift are shrinking and expanding, while Kenyan lakes are expanding. The en-dorheic lakes suffered the most fluctuations due to anthropogenic factors at the expense of loss of forest and woodlands in their watershed. While the lakes’ water quality related to the morphological changes are given less attention, the predicted 12 m drop of Lake Turkana due to projects in the Omo catchment did not materialize.