In coastal estuarine embayments, retention of water masses due to coastal topography may result in an increased contribution of continental organic matter in food webs. However, in megatidal embayments, the effect of topography can be counterbalanced by the process of tidal mixing. Large amounts of continental organic matter are exported each year by rivers to the oceans. The fate of terrestrial organic matter in food webs of coastal areas and on neighboring coastal benthic communities was therefore evaluated, at multi-trophic levels, from primary producers to primary consumers and predators. Two coastal areas of the French Atlantic coast, differing in the contributions from their watershed, tidal range and aperture degree, were compared using carbon and nitrogen stable isotopes (d13C and d15N) during two contrasted periods. The Bay of Vilaine receives large inputs of freshwater from the Vilaine River, displaying 15N enriched and 13C depleted benthic communities, emphasizing the important role played by allochtonous inputs and anthropogenic impact on terrestrial organic matter in the food web. In contrast, the Bay of Brest which is largely affected by tidal mixing, showed a lack of agreement between isotopic gradients displayed by suspended particulate organic matter (SPOM) and suspension-feeders. Discrepancy between SPOM and suspension-feeders is not surprising due to differences in isotopes integration times. We suggest further that such a discrepancy may result from water replenishment due to coastal inputs, nutrient depletion by phytoplankton production, as well as efficient selection of highly nutritive phytoplanktonic particles by primary consumers.