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Shallow inland water bodies in Malawi continue to be threatened by various environmental challenges despite their importance to the fisheries industry. Due to the complex interaction between natural and anthropogenic disturbances, disentangling the effect of the two may be a complicated process. The littoral zone of most water bodies is important in environmental reconstructions including pollution and lake level monitoring. This study used a littoral zone, transect-based approach employing multi-proxy palaeolimnological techniques to reconstruct recent environmental change (ca. 100 yrs.) in Lake Malombe in the Malawi Rift, East Africa. The results of the study could inform fisheries management in Lake Malombe, which experienced a catastrophic decline in fish stocks. Results support documentary evidence for the complete desiccation of the lake less than 100 years ago. Subsequently, there is evidence for accelerated eutrophication in the recent past. In light of these results, it is concluded that transect sampling approaches rather than relying on single core measurements, and the need for careful consideration of the types of proxy, are significant considerations in palaeoenvironmental reconstructions.