Inputs of heat and moisture through surface energy exchanges are important in the evolution of diurnally modulated thunderstorms. As part of the Maritime Continent Thunderstorm Experiment (MCTEX) conducted on the Tiwi Islands, northern Australia, we measured the surface energy exchanges above the dominant surface types (savanna, grassland, forest and shallow tidal strait). Measurements were made during the monsoon transition period (October--December) using the Bowen ratio and the aerodynamic techniques. A full radiation balance was measured at the Savanna site, where the surface albedo was determined as 0.19. The surface energy exchanges showed broad similarities between the sites, with comparable high net radiation totals averaging 11.8 MJ.m-2.day-1 over the terrestrial sites. The substrate heat fluxes were large at the Tidal strait (4.21 MJ.m-2.day-1) due to the high rates of energy absorption into water. The partitioning of net radiation into sensible and latent heat fluxes was controlled primarily by surface characteristics such as soil moisture and vegetation cover, with Bowen ratios averaging 1.08, 0.65, 0.5 and 0.40 for grassland, forest, savanna and tidal strait sites, respectively. A higher Bowen ratio was recorded at the Grassland site as this was during an earlier period that was much drier. Strong relationships were observed between the total surface convective fluxes and boundary layer development (e.g., the lifting condensation level) and between the magnitude of the daytime surface sensible heat flux and the onset time of thunderstorm convection. Observed terrestrial surface fluxes of moisture (averaging 165--265 W.m-2) were deemed insufficient for observed thunderstorm initiation and suggest that sea breeze advection of moisture is necessary. Tiwi Island thunderstorms were shown to represent a dynamic system where surface fluxes are important in generating a boundary layer sufficient to initiate the thunderstorms but where feedbacks between thunderstorms and surface fluxes eventually help terminate the storms.