The spread of invasive alien species is identified as one of the most important threats to freshwater ecosystems as they can modify their trophic structure, biomass and flows. The lower Saône River is one of the most biologically productive waterways in France. It has been in strong interaction with a wide range of human activities such as fisheries for at least three millennia. To implement an ecosystem based approach, an Ecopath static trophic model was used for the first time in this river to quantify the role of three invasive or expanding species over two contrasted periods (1988–1993 and 1994–2005). The parameters used in the model integrate on the one hand catch data from fishers (professional, amateur fishing gear users, and anglers), and on the other hand the available literature data on species biomass, diet and the expert assessments of scientists and managers. Species such as the filtering Asian clam Corbicula fluminea may explain the triggering of the ecosystem shift towards a functioning where summer phytoplankton blooms are rarer. In the high trophic levels, the great cormorant Phalacrocorax carbo appears to have low trophic impact while the development of a large population of European catfish Silurus glanis has a strong effect, maintaining important trophic flows in the ecosystem in substitution for the decrease in angling landings.