There are 104 hydroelectric facilities proposed to be installed in the watersheds that feed the Pantanal, a vast floodplain wetland located mostly in Brazil. The Pantanal is host to 23 long‐distance migratory fish species that ascend upland tributaries to spawn. A Geographic Information System was used to predict the impact of hydroelectric dams on potential migration routes for these species. Both anthropogenic (hydroelectric dams) and natural barriers were included in the analysis. Natural barriers were identified by river slope. Critical river slopes of 10 and 25%, above which fish were predicted to be incapable of ascending, were modeled as natural barriers. Based on this model, we show that between 2 and 14% of rivers in the Pantanal watershed are naturally blocked to fish migration. An additional 5 to 9% of rivers are currently blocked due to 35 existing hydroelectric facilities. If all proposed dams are built, the area flooded by new reservoirs will triple and the river kilometers blocked will double, blocking 25 to 32% of the river system to fish migration. The Taquari and Cuiabá River sub‐basins will be the most impacted, each having more than 70% of their rivers blocked. The impact of individual proposed facilities on the loss of migration routes is related to their proximity to existing barriers. Fourteen of the proposed dams are upstream from existing barriers and will therefore not further restrict long‐distance fish migration routes while proposed dams are predicted to close an additional 11,000 to 12,000 km of river channels.