We analyze the invisibility of fisheries and inadequacy of fishers’ participation in the process of hydropower development in the Amazon, focusing on gaps between legally mandated and actual outcomes. Using Ostrom’s institutional design principles for assessing common-pool resource management, we selected five case studies from Brazilian Amazonian watersheds to conduct an exploratory comparative case-study analysis. We identify similar problems across basins, including deficiencies in the dam licensing process; critical data gaps; inadequate stakeholder participation; violation of human rights; neglect of fishers’ knowledge; lack of organization and representation by fishers’ groups; and lack of governmental structure and capacity to manage dam construction activities or support fishers after dam construction. Fishers have generally been marginalized or excluded from decision-making regarding planning, construction, mitigation, compensation, and monitoring of the social–ecological impacts of hydroelectric dams. Addressing these deficiencies will require concerted investments and efforts by dam developers, government agencies and civil society, and the promotion of inter-sectorial dialogue and cross-scale participatory planning and decision-making that includes fishers and their associations.