Hydrological regimes, including inter- and intra-annual water level fluctuations, are key drivers of productivity and structure in freshwater ecosystems in Africa, where inland fisheries are a vital source of income and protein. Using a synthesis of seventeen standardized food web models of thirteen African lakes and reservoirs, this study explored the relationship between inter- and intra-annual water level fluctuations and sixteen ecological attributes associated with ecosystem configuration, productivity and maturity. The satellite and gauge data compiled indicate that climate driven long-term changes in the water level fluctuation regimes of African lakes have already taken place. Ten of the thirteen systems studied exhibited an increase in seasonal water level fluctuation magnitude over the time period for which data were available. Principle component and regression analyses revealed that relative water level fluctuations are a key physical indicator of African lakes and are significantly correlated with nearly all of the ecological attributes studied. In fact, water level fluctuations alone are a better predictor of ecological attributes than are combinations other physical characteristics. Water level fluctuations have a particularly strong influence on production, biomass, and fish diversity. Highly fluctuating systems differ from more stable systems in that they carry more of their production and biomass at lower trophic levels. These findings have ramifications for the productivity and composition of African lake fisheries, stressing that environmental consideration must be incorporated into management plans.