The Bay of Seine (English Channel) is a highly impacted ecosystem concerned by a lot of human activities and stakeholder interventions. It is subjected to heavy historic anthropogenic pressures and the emergence of new human activities: fishing, harbour extension, aggregate extraction, deposit of redged sediment, offshore windfarm. By contrast, this area showed high level of protection of natural heritage mainly Natural Reserve and Natura 2000 sites. It is also sensitive to climate change. Nevertheless, in the Seine Estuary, there is an accumulation of European, National, Regional and Industrial research projects ensuring a high level of scientific knowledge in this area. The available data are analysed by food-web modellers, looking at functional and holistic properties derived from the Ecological Network Analysis indices. Trophic models describe the interaction between species at different trophic levels and are based on the quantification of flow of energy and matter in ecosystems. Two main characteristics emerged: contrast of zones with low and high abundances and biomasses of benthos, and presence of spot of abundances and biomasses which remained a high potential source of prey for high trophic levels. Moreover, benthic habitats show high resilience while pelagic, fish and bird compartments have been affected by clear global changes. The conclusions exhibit the need to integrate human pressures of the functioning of complex ecosystems and their integration into social-ecological system, with a special interest in interactions of scales, uncertainty estimation, possible use of scenarios and indirect interactions between decisions, through global changes.