We investigated the food web structure of the Salses-Leucate Lagoon (northwestern Mediterranean) through delta C-13 and delta N-15 analysis of its benthic macrofauna and potential food sources. This lagoon was heavily human-modified during the 1970s, allowing permanent exchange with the open sea and an increase in salinity from that time. As a result, it exhibits a much less marked salinity gradient than the neighbouring lagoon ecosystems, which Suggests a priori that its food web structure is more homogeneous. In this environmental context, we assessed spatial variability in the isotopic composition of non-vagrant macrofauna in Salses-Leucate in relation to degree of connection with the open sea, anthropogenic inputs and the presence of oyster aquaculture. Overall, the main trophic pathway is based on suspended particulate organic matter and sedimented organic matter. However, there were marked spatial differences (at different scales) in both delta C-13 and delta N-15 values of macrofauna, which suggests an important feeding plasticity within each category of primary consumers at a small spatial scale. delta C-13 data showed that the contributions of the different food sources to the diet of primary consumers changed depending on distance from continental inputs, connection with the open sea and local primary producer coverage. Small-scale delta N-15 variability revealed a very localised influence of anthropogenic nitrogen output. Regarding the possible effect of aquaculture, the isotopic ratios of sediment and macrobenthos were not modified underneath the oyster lines with respect to the neighbouring area. Conversely, the isotopic signature of consumers living on the oyster lines contrasted with those living underneath. Therefore, our results suggest that a decoupling exists between the trophic pathways that occur in the water column and on the soft bottom of this shallow water ecosystem.