Abstract The exchange of internal energy between the warm water pools of the tropical oceans and the overlying atmosphere is thought to play a central role in the evolving climate system of the earth. Spatial displacements of the warm water pools are observed on annual and interannual time scales, the latter most notably in the Pacific in association with ENSO. Whether such variations are also associated with net changes in pool energy content is investigated. Extending the work of Niiler and Stevenson and Walin who considered the time mean energy budgets for volumes bounded by an isotherm, the time-dependent version of their equation is analyzed in which the main terms involve the time variations of pool volume and average temperature, net energy exchange between the pool and overlying atmosphere, and the turbulent ocean fluxes across the pool boundaries. The dominant signal in the mean seasonal energy budgets of the warm pools is an approximate balance between the annual variation of air pool heat excha...