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The volcanic and tectonic lakes of the eastern branch of the African Great Rift Valley are exposed to multiple stressors and characterised by different levels of hydrological connectivity. Past volcanic activity generated endorheic basins, in which the nature of the bedrock, its connection with groundwater, and local climatic conditions, favoured the formation of highly alkaline soda waters. While little is known about their nutrient dynamics, most lakes in this area experience considerable microbial blooms and harbour diverse and specifically adapted microbial populations, some of which could embody novel biotechnological potential. Here we review the geochemical and (micro)biological features of a cluster of lakes distributed within the East African Rift, ranging from fresh to hypersaline, under different levels of hydrological connectivity. Possibly no other location on Earth has a comparable range of lake types in close proximity to each other and representing such a remarkable microbial biodiversity. Environmental heterogeneity and habitat connectivity among adjacent aquatic ecosystems may have positive implications in terms of regional environmental stability by enhancing the overall carrying capacity, i.e. the resilience to various forms of impact, contributing to biodiversity protection. Within these ecosystems, microbial processes encompass the entire basis of their primary production, in particular those driven by cyanobacteria. Combining a multi-disciplinary ecohydrological approach with a biogeochemical investigation of the principles underlying their functioning, our study can contribute to the development of appropriate environmental protection measures to effectively maintain their natural capital.