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Incompatible land use is a major contributor to ecosystem degradation, and is often exacerbated by climate change impacts. We investigate Lake Basotu, Tanzania as a case study where natural lake variability has been affected by agricultural land use. Comparisons between a satellite-derived history of lake surface area, local precipitation records, and corresponding anthropogenic activity show the impacts of agricultural and historical practices. We argue that insufficient consideration to the wider ecological impacts of large agricultural projects has lasting implications. This is particularly true in semi-arid environments where food production demands need to be continuously met. In the future, major conservation strategies should be investigated to maintain the environmental integrity and sustainability of freshwater resources.