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This report summarizes the finding of the InHabit project on the importance of atmospheric nitrogen deposition in affecting the chemical composition of lake water and in eventually altering the biological communities living in them. Previous deliverables (I2d5, Id26 and I2d7) have shown that; 1. in both regions studied in the InHabit project (Piedmont and Sardinia), atmospheric deposition of nitrogen compounds is relevant; 2. the flux of nitrogen from the atmosphere to the ecosystem is markedly larger in Piedmont than in Sardinia; 3. models of the dynamic behavior of nitrogen in forested catchments indicates that Piedmon soils are mainly N-saturated, so that nitrogen carried by atmospheric deposition can be released form forest soil to the surface water; 4. in Sardinia, soil are less saturated, but a part of the deposited nitrogen is still carried to surface water; 5. trend analysis of deposition and stream water revealed that nitrogen deposition is stable or slightly decreasing in recent years, both in atmospheric deposition and in stream water; 6. the importance relative importance of N deposition is relevant for sites in or close to reference conditions; 7. the relationships between environmental variables and organisms belonging to the four biotic communities used to define the lake's ecological quality, according to provisions of the Italian legislation (D.Lgs. 260, November 2010) and the European Water Framework 2000/60 differ depending on the biological quality element considered; 8. phytoplankton community shows the clearer responses: according to the result of multivariate analysis, total nitrogen and ammonium nitrogen are among the most significant factors explaining the relationships among phytoplankton orders, species and environmental variables. In particular, cyanobacteria increased considerably with increasing availability of ammonium nitrogen. Conversely, high concentrations of this compound suppress the development of diatoms. On the basis of those results, which are summarized in this deliverable, we focused on the effect of different levels of nitrogen in lakes with low phosphorus concentration, slightly affected by direct trophic pressure and close to the reference conditions. The comparison between two lakes in Piedmont with low P concentration and high N concentration with two reservoirs in Sardinia with low levels of both nutrients shows that the formers are dominated by diatoms and the latter by dynophytes. Two reservoirs in Piedmont with high N levels are also dominated by diatoms. In spite of the small number of lakes studied, it seems that dynophytes are more fitted to low N lakes, probably because of their ability to use an heterotrophic metabolism, while lakes in reference conditions are generally considered to be dominated by oligotrophic diatoms, Our findings call for deeper studies on reference conditions in the Mediterranean ecoregion, because they suggest that lakes not affected by direct trophic pressure, i.e. reference lakes, may host different diatom communities depending on the amount of nitrogen deposition they receive.