Tropical countries are experiencing a hydropower development boom, yet environmental assessments of mega-dams fail to properly estimate their ecological impacts. We quantified the amount of forest and biodiversity loss associated with 49 existing (ED) and planned dams (PD) in Brazilian Amazonia, and assessed their biodiversity-hydropower tradeoffs. We projected the archipelagic configuration likely to be created by each PD and estimated local extinction rates for 96 vertebrate species based on species-area relationships from a large hydroelectric reservoir we studied. Once built, these dams will inundate ~1.3 Mha of forests, creating 12,457 islands which are expected to lose 89.9% of their vertebrate populations. Although forest loss within and around the reservoirs is higher in EDs, PDs will on average result in greater biodiversity loss and lower hydropower installation capacity. We call for decisive rethinking by policy-makers and energy strategists about the detrimental impacts of future hydroelectric infrastructure in lowland tropical forests worldwide. Tropical countries are experiencing a hydropower development boom, yet environmental assessments of mega-dams fail to properly estimate their ecological impacts. We quantified the amount of forest and biodiversity loss associated with 49 existing (ED) and planned dams (PD) in Brazilian Amazonia, and assessed their biodiversity-hydropower tradeoffs. We projected the archipelagic configuration likely to be created by each PD and estimated local extinction rates for 96 vertebrate species based on species-area relationships from a large hydroelectric reservoir we studied. Once built, these dams will inundate ~1.3 Mha of forests, creating 12,457 islands which are expected to lose 89.9% of their vertebrate populations. Although forest loss within and around the reservoirs is higher in EDs, PDs will on average result in greater biodiversity loss and lower hydropower installation capacity. We call for decisive rethinking by policy-makers and energy strategists about the detrimental impacts of future hydroelectric infrastructure in lowland tropical forests worldwide.