In 2007, unusually low values of dissolved inorganic nitrogen (DIN) were recorded. Combined with stable values of soluble reactive phosphorus (SRPs), low DIN led to a reduction of about one order of magnitude in the DIN:SRP atomic ratio with respect to the past and to 2008. G. longissima accumulated C, N and P more than the other species and A. corallinum proved to be less demanding. Sediment OM was lower in the autumn of years characterized by dystrophy, confirming that summer dystrophic events coincided with maximum energy dissipation in this ecosystem. However, as soon as OM and DIN values increased (2008), the vegetation shifted towards blooms of G. longissima and C. linum, while A. corallinum almost disappeared. The results sustain the hypothesis that the bloom of A. corallinum was due to a decline in DIN that limited G. longissima, and to intense turbidity of the water caused by microphytes that developed after the dystrophic event of summer 2006. The latter probably limited the development of C. linum, which could only develop at the edges of the lagoon.