Abstract: Floodplain lakes are widespread and ecologically important throughout tropical river systems, however data are rare that describe how temporal variations in hydrological, meteorological and optical conditions moderate stratification and mixing in these shallow lakes. Using time series measurements of meteorology and water‐column temperatures from 17 several day campaigns spanning two hydrological years in a representative Amazon floodplain lake, we calculated surface energy fluxes and thermal stratification, and applied and evaluated a 3‐dimensional hydrodynamic model. The model successfully simulated diel cycles in thermal structure characterized by buoyancy frequency, depth of the actively mixing layer, and other terms associated with the surface energy budget. Diurnal heating with strong stratification and nocturnal mixing were common; despite considerable heat loss at night, the strong stratification during the day meant that mixing only infrequently extended to the bottom at night. Simulations indicated that the diurnal thermocline up and downwelled creating lake‐wide differences in near‐surface temperatures and mixing depths. Infrequent full mixing creates conditions conducive to anoxia in these shallow lakes given their warm temperatures.