Abstract. Precipitation variability and complex topography often create a mosaic of vegetation communities in mountainous headwater catchments, creating a challenge for measuring and interpreting energy and mass fluxes. Understanding the role of these communities in modulating energy, water and carbon fluxes is critical to quantifying the variability in energy, carbon, and water balances across landscapes. The focus of this paper was: (1) to demonstrate the utility of eddy covariance (EC) systems in estimating the evapotranspiration component of the water balance of complex headwater mountain catchments; and (2) to compare and contrast the seasonal surface energy and carbon fluxes across a headwater catchment characterized by large variability in precipitation and vegetation cover. Eddy covariance systems were used to measure surface fluxes over sagebrush (Artemesia arbuscula and Artemesia tridentada vaseyana), aspen (Populus tremuloides) and the understory of grasses and forbs beneath the aspen canopy. Peak leaf area index of the sagebrush, aspen, and aspen understory was 0.77, 1.35, and 1.20, respectively. The sagebrush and aspen canopies were subject to similar meteorological forces, while the understory of the aspen was sheltered from the wind. Missing periods of measured data were common and made it necessary to extrapolate measured fluxes to the missing periods using a combination of measured and simulated data. Estimated cumulative evapotranspiratation from the sagebrush, aspen trees, and aspen understory were 384 mm, 314 mm and 185 mm. A water balance of the catchment indicated that of the 699 mm of areal average precipitation, 421 mm was lost to evapotranspiration, and 254 mm of streamflow was measured from the catchment; water balance closure for the catchment was within 22 mm. Fluxes of latent heat and carbon for all sites were minimal through the winter. Growing season fluxes of latent heat and carbon were consistently higher above the aspen canopy than from the other sites. While growing season carbon fluxes were very similar for the sagebrush and aspen understory, latent heat fluxes for the sagebrush were consistently higher, likely because it is more exposed to the wind. Sensible heat flux from the aspen tended to be slightly less than the sagebrush site during the growing season when the leaves were actively transpiring, but exceeded that from the sagebrush in May, September and October when the net radiation was not offset by evaporative cooling in the aspen. Results from this study demonstrate the utility of EC systems in closing the water balance of headwater mountain catchments and illustrate the influence of vegetation on the spatial variability of surface fluxes across mountainous rangeland landscapes.