The rapid expansion of hydropower dam construction in tropical rivers has significantly impacted fish biodiversity and fisheries. The construction of the Santo Antônio and Jirau dams on the Madeira River in 2012 resulted in immediate changes to fish assemblages, but the long-term effects remain largely unexplored. To address this, we analyzed fish assemblages before, shortly after, and long after dam construction. Over 19 years, we collected fish from upstream, within reservoirs, and downstream of dams using gillnets. Hierarchical Models of Species Communities (HMSC) revealed distinct responses among fish in each section, with all sections showing long-term declines. Species richness initially increased in the upstream and reservoir sections but later decreased. In the downstream section, species richness steadily declined through time. The upstream section experienced aa temporary rise in intermediate life history strategists and planktivorous fish, followed by a long-term reduction in all functional groups. In the reservoir section, fish occurrence initially surged, particularly among planktivores, but declined in the long term. The downstream section saw a steady decline in fish groups, especially intermediate strategists and herbivores. Our study reveals the complex impacts of hydropower dam construction on fish assemblages in the Madeira River. While there were initial increases in probability of occurrence of certain taxonomic and functional groupings in some areas, these were temporary, eventually leading to significant long-term declines across all sections of river. Results highlight the persistent ecological consequences of large-scale hydropower projects to local fisheries and biodiversity.