This study assessed the influence of land cover changes on evapotranspiration and streamflow in small catchments in the Upper Xingu River Basin (Mato Grosso state, Brazil). Streamflow was measured in catchments with uniform land use for September 1, 2008 to August 31, 2010. We used models to simulate evapotranspiration and streamflow for the four most common land cover types found in the Upper Xingu: tropical forest, cerrado (savanna), pasture, and soybean croplands. We used INLAND to perform single point simulations considering tropical rainforest, cerrado and pasturelands, and AgroIBIS for croplands. Converting natural vegetation to agriculture substantially modifies evapotranspiration and streamflow in small catchments. Measured mean streamflow in soy catchments was about three times greater than that of forest catchments, while the mean annual amplitude of flow in soy catchments was more than twice that of forest catchments. Simulated mean annual evapotranspiration was 39% lower in agricultural ecosystems (pasture and soybean cropland) than in natural ecosystems (tropical rainforest and cerrado). Observed and simulated mean annual streamflows in agricultural ecosystems were more than 100% higher than in natural ecosystems. The accuracy of the simulations was improved by using field-measured soil hydraulic properties. The inclusion of local measurements of key soil parameters is likely to improve hydrological simulations in other tropical regions.