Dramatic changes in Lake Malawi’s ecological history are associated with the major lake level fluctuations. Today, and for the past ~60-70 thousand years, L. Malawi has been a strongly stratified lake, with very clear waters and low nutrient concentrations in surface waters intersecting the steeply sloping (fault bounded) rocky lake floors that ring the basin. These conditions have been conducive to the evolution of an ecosystem dependent on visual cues for mate recognition and predation, especially among the hyperdiverse cichlid fish that dominate the nearshore environment today. During the many megadrought episodes of the lake’s history however, nearshore and offshore ecological conditions would have been very different. The lake would have been reduced to an extent that the rocky habitats associated with major border faults would have no longer ringed the lakeshore (muddy bottoms would have prevailed along most coasts). The much smaller lake would have been well-mixed and turbid with algae in surface waters (e.g. a green lake, rather than a blue one). The combination of these factors would have severely impacted cichlid communities and other components of the nearshore ecosystem, and probably contributed to a significant loss of biodiversity during these times. Lake Malawi’s evolutionary history as a hotspot of biodiversity must be understood within the framework of this dramatic history, especially in comparison to its sister Lake Tanganyika, where the impact of climatically driven lake level fluctuations was most likely much less dramatic. The rapidity of ecological change evident in parts of the paleoecological record of Lake Malawi also gives us pause to reflect on how quickly anthropogenically driven changes in lake level (for example from water diversion from agriculture) or nutrient inputs might also impact this extraordinary ecosystem.