In naturally flowing waters, communities are expected to increase their taxonomic and functional diversity as well as increase the complexity of food web architecture along the longitudinal gradient from headwaters to mouth. However, these theories do not necessarily apply to dammed rivers. We analysed fish communities at 12 locations along the 1700 km stretch of the transnational Uruguay River. We determined species richness, beta-diversity and its components (turnover and nestedness), trophic diversity, and isotopic niches at community level, with particular focus on areas upstream and downstream of the four existing dams. We estimated trophic diversity metrics based on diet analysis, and isotopic niche breadth based on Bayesian isotopic niche models. We detected consistent longitudinal changes, supporting predictions from the River Continuum Concept. However, taxonomic richness, trophic diversity, and isotopic niche decreased abruptly immediately downstream of dams, and the component contributing the most to beta diversity was turnover, with the highest values occurring mainly after the cascade of dams in the upper Uruguay River, fitting expectations from the Serial Discontinuity Concept. The dam-free stretches of the Uruguay River allowed the recovery of ecological diversity as fish richness and trophic and isotopic niche increased. The negative impacts of dams should urgently be considered in the Neotropics, where many large dams are projected.