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Lakes are important in supporting ecosystem services and livelihoods. However, their food webs and ecological functioning are continuously threatened by anthropogenic influences. Food web models have been widely used in studying trophodynamics, fisheries impacts, and ecological functioning of temperate lakes, but less often in Afrotropical lake systems. We used Ecopath mass‐balanced trophic models annually in 1999, 2010, and 2020 to assess trends in ecosystem function, and the impact of fisheries on the Lake Baringo Ecosystem, a shallow freshwater lake in Kenya. Pre‐balance (PREBAL) and Pedigree analyses supplemented Ecopath models. Model input data were from field sampling, published and gray literature. Food web trophic models indicated a bottom‐up grazer and detrital food chains in all 3 years. Odum's ecosystem development indicators (total productivity to total biomass and total respiration ratios; TPP/TB and TPP/TR) showed that the lake was in a low to intermediate developmental stage, with room for bio‐manipulation, and a highly reduced mean transfer efficiency (TE) (6.4%–0.49%) indicated low trophic transfer of internal production. System omnivory (SOI) and connectance (CI) indices that varied among years indicated temporal variation in food web complexity. Indices of system resilience (overhead and ascendency) indicated an increasing potential for the lake to recover from perturbations. The mean trophic level of the catch (MTLc) increased from 1999 to 2010 and decreased in 2020, by fishing down the food chain as fishing pressure increased. Oreochromis niloticus, an endemic cichlid, was the keystone species (KSi >0) controlling community structure, while the lungfish Protopterus aethiopicus, the top predator in the lake, was not a keystone species (KSi <0). We recommend an integrated approach to lake management that incorporates watershed regulations, regulates fishing effort on the keystone species (O. niloticus), and monitors water quality for sustainable management of the Lake Baringo ecosystem. [ABSTRACT FROM AUTHOR]