The eddy covariance (EC) technique has been widely used to measure ecosystem surface energy fluxes. However, with a relatively small representative area (footprint), errors are often introduced when upscaling EC data based on variables derived from large-footprint satellite products. Furthermore, EC measurements often fail to close the energy balance in ecosystems such as wetlands. As an alternative to EC, large aperture scintillometers (LAS) have been used to measure sensible heat fluxes (H) over representative areas comparable to the resolution of large-scale satellite images. However, because LAS measurements are based on semi-empirical simulations, their accuracy needs further evaluation across ecosystems. Changes in hydrology on the land surface significantly alter measurement conditions as well as the processes of energy transfer, and thus, may affect the accuracy of energy measurements from LAS. To address this issue, we compared the LAS-measured H (HLAS) to EC-derived H (HEC) in a seasonally inundated wetland within Everglades National Park. Overall, the HLAS was 7.1 ± 0.3 (SE) % greater than HEC, and the ratio of HLAS to HEC remained similar between the wet season, when the ecosystem was inundated, and the dry season. However, inundation, as a thermal buffer in the system, reduced the magnitude of H in the wet season and resulted in a smaller difference of seasonal H budget estimates between LAS and EC measurements. Because of the homogenous land surface at our site, the discrepancies between HLAS and HEC could not be explained by footprint mismatch. Compared to the energy balance closure calculated with HEC, the closure calculated with HLAS was improved by 6% during the dry season but remained similar during the wet season. Overall, we conclude that LAS can be a reliable approach to measure H in wetland ecosystems and its measurements were stable with seasonal hydrological changes.