Sagebrush ecosystems consist of different communities of species and subspecies of sagebrush marked by distinct ecotones along elevation gradients, yet few studies have quantified how ecosystem-scale carbon dioxide (net ecosystem exchange, NEE) and water fluxes (evapotranspiration, ET), as well as their environmental drivers, vary among communities dominated by different sub/species of sagebrush at daily and seasonal time scales. To address this knowledge gap, we measured daytime (6 a.m.–6 p.m.) NEE and ET using a tent chamber and associated environmental drivers in three sagebrush communities spanning an elevation gradient of 1 425–2 111 m at the Reynolds Creek Critical Zone Observatory in southwestern Idaho. Daytime NEE and ET were greatest at the highest elevation (snow-dominated) site during the study period except NEE in June. By late summer, NEE declined by > 80% at the lower (rain-dominated) sites but only 50% at the highest site, compared with maximal values in June. In contrast, ET declined ∼95% in late summer compared with June at all three sites. Ecosystem-scale NEE and ET were mainly controlled by soil moisture and vapor pressure deficit at the rain-dominated sites and by deep soil moisture and air temperature at the snow-dominated site. Cumulative (June–August) modeled daytime NEE was greatest at the midelevation site, whereas cumulative daytime ET was greatest at the highest-elevation site. Ecosystem models often assume that sagebrush landscapes are homogeneous and do not differ in fluxes and controls, yet our data demonstrate that there are fundamental differences in CO₂ and water fluxes and their controls among different shrub communities that should be accounted for in these models.