Restoration of the ecological continuity of rivers has become a strong ecological issue. In some cases, it may lead to the dismantling of dams, but ecological consequences for estuarine ecosystems are poorly known. Notably, by increasing sediment and nutrient retention in reservoirs, dams can alter the influx of terrestrial subsidies to estuarine food webs. Here, we assessed the trophic functioning of the megatidal estuary of the river Sélune (bay of Mont-Saint-Michel, France) before the removal of two large dams on the river. Both estuarine benthic invertebrate and bentho-demersal fish faunas were characterized at two periods (spring and autumn 2017) and food web described by means of stable isotope (nitrogen and carbon) and fish gut analyses. Macrobenthic fauna was typical of European estuaries, with low species richness because of high physical constraints (highly variable salinity, strong currents, high altitude) prevailing in the area. High abundances and biomasses were observed in the two downstream sectors under the bay influence providing them a feeding interest for juvenile fish. Two species of gobies (Pomatoschistus microps and Pomatoschistus minutus), juvenile sea bass (Dicentrarchus labrax) and juvenile flounder (Platichthys flesus) dominated the fish fauna. Food web was mostly fueled by local primary production, predominantly microphytobenthos. Macrobenthic invertebrates (Corophium arenarium or Bathyporeia pilosa) but also harpacticoid copepods and mysids in autumn were the major prey and constitute the primary consumer level of the food web, the fish being at the top as secondary consumers. The analysis of the trophic niche of fish and their overlaps gave elements on the respective feeding strategies and inter-specific competitions.