The implementation of the European Water Framework Directive (WFD) has led to the development of various biotic indices in order to assess the ecological status of aquatic ecosystems. These indices are mainly based on the structure of ecological communities. The main underlying assumption of such an approach is that structural features of selected ecological communities are representative of the ecological functioning of the ecosystem. In particular, the ecological status of transitional waters has to be assessed using fish-based indicators (FI) which are computed using observation data on species diversity and abundance. Concurrently, stability, maturity and resilience features of ecosystems are often discussed using indices provided by Ecological Network Analysis (ENA). ENA is not only based on structural elements of ecological communities but also on a functional description of the ecosystem centred on energy flows. However, to conclude on “whether some attribute of ecosystem networks might provide an appropriate and useful indicator of system performance” (Ulanowicz 2004), ENA approaches must be compared with other existing methods of assessing ecological quality (Christian et al., 2005). The purpose of this work is to discuss results of both approaches applied on 5 French estuarine areas.