Despite the importance of headwater basins for western United States’ water supply, these regions are often poorly understood, particularly with respect to quantitative understanding of evapotranspiration (ET) fluxes. Heterogeneity of land cover, topography, and atmospheric patterns in these high-elevation regions lead to difficulty in developing spatially distributed characterization of ET. As a significant fraction of the water budget, ET contributes to overall water and energy availability in the basin. Using an eddy covariance tower in the East River Basin, a Colorado River headwaters basin, this study improves the quantification of water and energy fluxes in high-elevation, complex systems to better constrain ET estimates and calculate overall water and energy budgets. The eddy covariance method estimates ET from years 2017 through 2019 at a saturated, riparian end-member site. During the late spring, summer, and early fall months, due to strong variations in lower atmospheric stability and evidenced by a less than 30% energy balance closure error in these months (within the range of closure error reported at other riparian locations) we conclude that the eddy covariance method is useful in high-elevation, complex areas such as the East River Basin and helps bound regional ET estimates. We also compared East River ET magnitudes and seasonality to two other eddy covariance towers (Niwot Ridge, CO and Valles Caldera, NM), with similar site characteristics, located in the Rocky Mountains. East River ET estimations are useful for constraining water budget estimates at this energy-limited site, which uses groundwater for up to 76% of ET in the summer months. This data is useful for constraining ET estimates in similar end-member locations; however, to better constrain ET estimates across the entire East River basin, additional sampling is needed. This study helps constrain both the energy and water budgets in locations that are underrepresented by observations and where indirect estimates of ET may perform poorly.