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We studied the changes of exergy and specific exergy with data of benthic macrofauna communities, periodically sampled along an estuarine gradient of eutrophication in the Mondego estuary (Western Portugal). Exergy estimates were calculated from organism biomass, based on weighing factors for the relative content of exergy per unit of biomass determined from DNA contents of organisms. Results were discussed in terms of both the macrofauna biomass production and the structural organisation of the system. Estimates for the exergy indices provided useful indications for the evaluation of environmental impact due to the eutrophication process. Different average values for the indices of exergy and specific exergy were estimated relatively to areas with different levels of eutrophication, in the 'spatial' gradient of eutrophication. Higher exergy levels and lower exergy content per unit of biomass (specific exergy) were associated to populations more stabilized or areas less perturbed. Additionally, the index of specific exergy seemed capable of providing indications for the qualitative alterations in the communities (in temporal and spatial terms) that go in the direction of the observations made in this ecosystem.