Evapotranspiration has been poorly characterized in the Altiplano, and the legal dispute over the status and use of the waters of the Silala River provided an opportunity for improving knowledge of this hydrological process, in a remote area with a lack of hydrometeorological data. Actual evapotranspiration (ETa) measurements using eddy covariance (EC) were performed in the riparian wetland (EC1) and over the alluvial deposits (EC2) of the Silala River basin, and in the Putana River wetland (EC3), with similar characteristics to the Silala River headwaters. The portable chamber method was used to characterize soil and plant evaporation near EC2. Satellite‐derived ETa estimates were evaluated with the in‐situ data, and used to investigate spatiotemporal dynamics of the wetland vegetation cover. At EC1 and EC3, annual ETa values were 703 and 841 mm, respectively; and satellite‐derived ETa showed differences of 5% and −35% from these values. ETa exhibited strong seasonal variations at EC1 and EC3, and was sensitive to precipitation at EC2. ETa did not follow the temporal evolution of the reference evapotranspiration at EC2, suggesting that lateral subsurface flow supports ETa in dry periods. Portable chamber measurements revealed that bare soil evaporation is the main component of ETa in the alluvial deposits. ETa data collected within the basin, as described in other papers of this special issue, allowed validation of a hydrological model used to estimate the basin's groundwater recharge, and estimation of the surface flow increase due to river channelization, which were important scientific evidence provided in the legal dispute.This article is categorized under: Science of Water > Hydrological Processes Science of Water > Methods