The afforestation of grasslands can alter different ecosystems’ functional processes; it affects the water balance due to the high water demand, caused by the increased productivity of the plantations, increase evapotranspiration, and reduces base flow of the basins. In Uruguay, there are two scenarios; the headwaters of the Tacuarembó River, where the area of plantations has increased for more than 30 years, and the headwaters of the Río Negro, where mainly grasslands are preserved without significant changes. This article evaluates the dynamics of grassland afforestation in the two basins, through the spatial and temporal analysis of historical trends with the use of remote sensors and considering the effect on water yield through field measurements, in the period 1984–2014. The spatial analysis shows an increase in the area of the forested basin, and the temporal analysis shows a reduction in the runoff coefficient due to the effect of the afforestation of pastures. Therefore, the movement from grassland to forest plantations reduces water flow considerably; this was identified through base flow measurements in the field with the integration of remote sensors. This allowed the observation of the relevant changes in the two basins studied, which may be related to climate change and human activities.