The construction of hydroelectric power plants results in habitat destruction and fragmentation, and this destruction is the major cause of the decline of endangered species, especially large mammals and especially carnivores. Brazil's energy matrix is based on approximately 70% hydroelectricity. Jaguar (Panthera onca) populations have been reduced or extinguished by human pressure. In Brazil it is considered a vulnerable species and it is critically endangered in the Atlantic Forest. In the Upper Paraná River (UPR), the reservoir filling of the Porto Primavera Hydroelectric plant (PPH) began in 1998, and flooded an area of approximately 2250 km². We evaluated the effects of the PPH reservoir filling on the jaguar population, spatial distribution and habitat suitability. We monitored 11 jaguars using radio telemetry over two periods (1992-1995 and 1998-2002). Jaguars’ home ranges increased significantly after reservoir filling (females: 78 km ² before [n = 8], 197 km ² after [n = 5]; male [n = 1]: 111 km ² before, 149 km ² after). The PPH filling suppressed approximately half of their suitable area and most jaguars were killed in retaliation for cattle predation as they commenced to occupy the most degraded areas. The remaining area of the UPR still holds approximately 50 adult jaguars. Therefore, the long-term species conservation depends on the preservation of the adjacent wetlands and on the restoration of forest patches. Our results can subsidize jaguar conservation and management plans in the UPR and show that habitat suitability modeling can be a useful tool for assessing environmental impacts.