The evaluation of extinction risk has typically focused on species, although a shift to a focus on ecosystem would appear to be an urgent priority for conservation planning. Here, we investigated how fish extinction modify the functioning of freshwater Amazonian ecosystems. We sampled the fish and environmental conditions of 63 streams in the eastern Amazon, and simulated extinction based on species vulnerability to habitat loss. The simulated extinction of vulnerable species led to a decrease in both the mean body size of the community and functional rarity, and culminated in abrupt losses of ecosystem function after 5% and 10% of extinction at local and regional scales. We provide robust predictions on the modification of the ecosystem following the extinction of fish species, which is a major step towards the development of effective conservation measures that help to prevent the loss of biodiversity and the potentially irreversible modifications of ecosystem function.