The Brazilian Amazon has been a focus of land development with large swaths of forests converted to agriculture. Forest degradation by selective logging and fires has accompanied the advance of the frontier and has resulted in significant impacts on Amazonian ecosystems. Changes in forest structure resulting from forest disturbances have large impacts on the surface energy balance, including on land surface temperature (LST) and evapotranspiration (ET). The objective of this study is to assess the effects of forest disturbances on water fluxes and canopy structural properties in a transitional forest site located in Mato Grosso State, Southern Amazon. We used ET and LST products from MODIS and Landsat 8 as well as GEDI-derived forest structure data to address our research questions. We found that disturbances induced seasonal water stress, more pronounced and earlier in croplands and pastures than in forests, and more pronounced in second-growth and recently burned areas than in logged and intact forests. Moreover, we found that ET and LST were negatively related, with a more consistent relationship across disturbance classes in the dry season than the wet season, and that forest and cropland and pasture classes showed contrasting relationships in the dry season. Finally, we found that canopy structural properties exhibited moderate relationships with ET and LST in the most disturbed forests, but negligible correlations in the least disturbed forests. Our findings help to elucidate degraded forests functioning under a changing climate and to improve estimates of water and energy fluxes in the Amazon degraded forests.