The role of surface and advective heat-fluxes on buoyancy driven circulation was examined within a tropical coral reef system. Measurements of local meteorological conditions as well as water temperature and velocity were made at six lagoon locations for two months during the austral summer. We found that temperature rather than salinity dominated buoyancy in this system. The data were used to calculate diurnally phase-averaged thermal balances. A one-dimensional momentum balance developed for a portion of the lagoon indicates that the diurnal heating pattern and consistent spatial gradients in surface heat fluxes creates a baroclinic pressure gradient that is dynamically important in driving the observed circulation. The baroclinic and barotropic pressure gradients make up 90% of the momentum budget in part of the system, thus, when the baroclinic pressure gradient decreases 20% during the day due to changes in temperature gradient this substantially changes the circulation, with different flow patterns occurring during night and day. Thermal balances computed across the entire lagoon show that the spatial heating patterns and resulting buoyancy driven circulation are important in maintaining a persistent advective export of heat from the lagoon, and for enhancing ocean-lagoon exchange.