© 2014, by the Association for the Sciences of Limnology and Oceanography, Inc. We characterize stratification patterns over diel, seasonal, and annual time scales in inshore and offshore regions of Lake Victoria, East Africa; determine conditions leading to horizontal exchanges; and, using surface energy budgets derived from local meteorological stations and two reanalysis products, address whether stratification depends on advective as opposed to local processes. The largest change in the surface energy budget occurred when winds intensified at the end of the long rains, with the wind’s intensification, duration, and spatial extent dependent on El Niño–Southern Oscillation cycles. These winds flush inshore waters and cause cross-basin upwelling similar to that observed in the deep African Great Lakes. Wedderburn numbers indicated mixing and cross-basin within-thermocline transport. The internal wave-induced mixing and enhanced latent heat fluxes of 2300 to 2400 W m22 contributed to the loss of seasonal stratification. Advection of cool water was required to balance the heat budget of northern offshore waters in the latter half of the southeast monsoon except in an El Niño year. Northern waters became weakly stratified after the southeast monsoon, with nocturnal winds contributing to heat transport and ventilation of the lower water column. Following the rainy season, downwelling by sustained southerly albeit low winds is a likely cause of the seasonal thermocline. Inshore waters are 0.2–1.5uC warmer than those offshore, conditions conducive to horizontal convective circulation except during onshore winds. The seasonal cycle of stratification and inshore–offshore and cross-basin exchanges are moderated by differential heating, cooling, and basin-scale thermocline tilting.