Small hydropower (SHP) facilities, defined variably but usually by installed capacities of <10–50 MW, are proliferating around the world, particularly in tropical and subtropical regions. Compared to larger dams, SHPs are generally viewed as having less environmental impact, although there has been little research to support that assertion. Numerous SHPs have been built, and many more are in development or proposed, in rivers that drain into the Pantanal, a world-renowned floodplain wetland system located mostly in Brazil. The upland tributaries are important sources of nutrients to the Pantanal, affecting the biological productivity of downstream floodplains. This study presents measurements from upstream and downstream of 25 current hydropower facilities, most of which are SHPs, throughout the upland watersheds of the Upper Paraguay River basin to reveal how these facilities may affect the concentrations and transport of nutrients in rivers flowing to the Pantanal. Artificial neural network models estimated the impact of building 80 future SHPs on nutrient transport into the Pantanal, based on observations at current facilities as well as the spatial distribution of future facilities. Overall impacts of current hydropower facilities were not large, and in most cases were indistinguishable based on comparisons between upstream and downstream. The short water residence times of reservoirs associated with SHPs likely explain their tendency to have little or no effect on nutrient transport. However, model predictions for hydropower facilities that may be built in the future, many on rivers with higher discharge and sediment loads, point to significant reductions in overall TN (8%) and TP (29%) transport, with potential negative consequences for river and floodplain productivity. Negative impacts may be either because the rivers carry low nutrient concentrations and are thereby sensitive to oligotrophication, or they are particularly important overall nutrient sources supporting ecosystem productivity in downstream rivers and floodplains. Together with a parallel study of sediment transport, these results support recommendations that several river systems presently lacking dams in their lower reaches should be excluded from future hydropower development to maintain the nutrient and sediment supply to the Pantanal.