Here, we investigated the effects of increasing concentrations of ozone ([O3]) on soybean canopy-scale fluxes of heat and water vapor, as well as water use efficiency (WUE), at the Soybean Free Air Concentration Enrichment (SoyFACE) facility. Micrometeorological measurements were made to determine the net radiation (Rn), sensible heat flux (H), soil heat flux (G0) and latent heat flux (λET) of a commercial soybean (Glycine max) cultivar (Pioneer 93B15), exposed to a gradient of eight daytime average ozone concentrations ranging from approximately current (c. 40 ppb) to three times current (c. 120 ppb) levels. As [O3] increased, soybean canopy fluxes of λET decreased and H increased, whereas Rn and G0 were not altered significantly. Exposure to increased [O3] also resulted in warmer canopies, especially during the day. The lower λET decreased season total evapotranspiration (ET) by c. 26%. The [O3]-induced relative decline in ET was half that of the relative decline in seed yield, driving a 50% reduction in seasonal WUE. These results suggest that rising [O3] will alter the canopy energy fluxes that drive regional climate and hydrology, and have a negative impact on productivity and WUE, key ecosystem services.