Escalating concerns about water supplies in the Great Basin have prompted numerous water budget studies focused on groundwater recharge and discharge. For many hydrographic areas (HAs) in the Great Basin, most of the recharge is discharged by bare soil evaporation and evapotranspiration (ET) from phreatophyte vegetation. Estimating recharge from precipitation in a given HA is difficult and often has significant uncertainty, therefore it is often quantified by estimating the natural discharge. As such, remote sensing applications for spatially distributing flux tower estimates of ET and groundwater ET (ETg) across phreatophyte areas are becoming more common. We build on previous studies and develop a transferable empirical relationship with uncertainty bounds between flux tower estimates of ET and a remotely sensed vegetation index, Enhanced Vegetation Index (EVI). Energy balance-corrected ET measured from 40 flux tower site-year combinations in the Great Basin was statistically correlated with EVI derived from Landsat imagery (r2 = 0.97). Application of the relationship to estimate mean-annual ETg from four HAs in western and eastern Nevada is highlighted and results are compared with previous estimates. Uncertainty bounds about the estimated mean ETg allow investigators to evaluate if independent groundwater discharge estimates are “believable” and will ultimately assist local, state, and federal agencies to evaluate expert witness reports of ETg, along with providing new first-order estimates of ETg.