Nutrient dynamics for phosphate, nitrate, ammonium and silicate have been simulated with the European Regional Seas Ecosystem Model in a Mediterranean lagoon. This generic model designed for the open sea can be usefully applied also to coastal lagoon ecosystems with minimum modifications. The annual cycles of the nutrients phosphate and silicate compare quite well with the observed ranges of variability. This does not hold for ammonium and nitrate where the increased concentrations could be attributed to external inputs from the land. Nutrient budgets calculated from the model results indicate some competition between phytoplankton and bacteria for nutrients, a common characteristic of lagoons. To further develop the model, an adaptation of the phytoplankton submodel to represent benthic primary production, as well as the modification of the benthic nutrient model to cope with anoxic events, are suggested.