EutrophicationTrophic structure a b s t r a c t Three Ecopath with Ecosim models were constructed to represent the eutrophication gradient along the south arm of the Mondego estuary (Portugal). Sampling was conducted in three areas representative of different environmental situations along the gradient: (a) a non-eutrophic area (Zostera noltii meadows), (b) an intermediate eutrophic area (macrophyte absent, although residual roots can still be found in the sediment, and the occasional formation of abundant macroalgae mats) and (c) a strongly eutrophic area (macrophyte community totally absent for at least a decade and strong, regularly occurring, blooms of Ulva spp.). Field, laboratory and literature information were used to construct the models, as well as empirical ecological knowledge gained from years of work on this system. Approximately 76 trophic groups (e.g. Phytoplankton and Zooplankton species), species and genera were included. These species were grouped into 43, 36 and 34 model groups for Zostera sp. meadows, intermediate eutrophic area and strongly eutrophic area, respectively. The groups were arranged by trophic similarity and habitat preferences; special distinction is given to macrofauna. Biomass, production, consumption, and diet are among the parameters used to describe each group. The sum of consumptions, exports, respiration, production, flow to detritus, total system throughput and annual rate of net primary production was always higher in the Zostera sp. meadows, followed by the strongly eutrophic area and, finally, by the intermediate eutrophic area.