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Lake Sonachi, Kenya, is a small alkaline-saline crater lake that over the past 175 years has experienced considerable fluctuations in lake depth ( Zmax 5 3‐18 m) and an alternation of meromictic and holomictic episodes lasting from a few years to several decades. Paleolimnological methods were used to reconstruct the long-term dynamics of algal and invertebrate communities in Lake Sonachi in relation to the historical evolution of their physical and chemical environment. Multivariate statistical analysis revealed only weak correlation between the stratigraphic distributions of fossil algal pigments, diatoms, and chironomid larvae in 210 Pb-dated sediment cores and the documented or reconstructed variation in lake depth, mixing regime, and surface-water conductivity. The eventful biological history of Lake Sonachi exemplifies the complexity of long-term community dynamics in tropical African soda lakes and reveals how phytoplankton community structure can exert direct control on benthic and planktonic invertebrate communities. The modest phytoplankton abundance and photosynthetic activity of Lake Sonachi when compared with other tropical African soda lakes represent recent lake conditions, resulting from a dramatic decline of filamentous cyanobacteria (e.g., Spirulina platensis) between the 1930s and 1970s and incomplete replacement by the small coccoid cyanobacteria (e.g., Synechococcus bacillaris), which are dominant today. This reduction in algal biomass favored benthic and planktonic invertebrates by reducing the prevalence of complete water-column anoxia associated with intense nighttime respiration of cyanobacterial blooms. Anoxia-intolerant halobiont chironomids expanded during an episode of low lake level (Zmax , 4 m), holomixis, and high conductivity (.9,000 m Sc m 21 ) in the late 1940s and 1950s, whereas they had failed to do so under similar conditions in the late 19th century when algal abundance was high. Planktonic cladocerans developed high population densities only during two short meromictic phases in the 1970s when conductivity was modest (3,000‐6,000 m Sc m 21 ) and algal abundance was low. The decline of filamentous cyanobacteria also increased water-column transparency but apparently did not increase benthic diatom abundance.