A description is given of the response of phytoplankton composition to eutrophication caused by an increase in fresh water flux in four Empordà salt marsh basins. Cyanobacteria and mixotrophic phytoplankters (especially haptophytes and dinoflagellates) are the most abundant organisms in these basins. Under stable conditions, cyanobacteria take competitive advantage of the lack of inorganic nitrogen caused by confinement. Mixotrophs dominate coinciding with water inputs. The importance of the allochthonous supply probably favours mixotrophs, which may also take nitrogen heterotrophically. The phytoplankton-invertebrate biomass ratio (P/I) and the chlorophyll-phytoplankton biovolume ratio (Chl/BV) respond differently to stabilisation of freshwater input, depending on the degree of eutrophy of the basins. Thus, in more eutrophic basins flux regulation causes an increase in P/I and a decrease in Chl/BV, indicating higher density of mixotrophs and lesser density of invertebrates. Less eutrophic basins respond in the opposite fashion.