The Food Web descriptor 4 (MSFD) is highlighted as the most difficult to implement. The extent to which sedimentary conditions shape trophic interactions of marine benthic assemblages is a gap of knowledge. It is hypothesized that the bottom-up differences in the sedimentary trophic status will shape the food web structure of benthic assemblages, in both estuarine and continental shelf environments. The benthic-mediated effects and the trophic position variation of macrobenthos and nematodes will be analysed using the ratios of stable isotopes of carbon and nitrogen. The biogeochemical parameters (chlorophyll, levels of metals, organic contaminants) and the microbial communities will be analyzed (by metagenomic sequencing) to assess the sediment trophic conditions. This research is a driver to create high specialized routines to monitor the D4 and its processes, contributing to attain scientific knowledge to this elements that define the state of marine environment.