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Phytoplankton and benthic vegetation biomass undergoes spatial-temporal changes in relation to their life cycle, but also to meteorological conditions, physical-chemical variables, organic input and internal dynamism. The main aim of this work was to observe the effect of all environmental variables on the vegetative dynamic process in a protected zone of a Mediterranean costal lagoon (Lesina lagoon, SE Italy). Seven samplings were performed from 2010 to 2012 at 30 sites for nutrient and chlorophyll analyses, while TOC measurements and wet biomass evaluation were performed at 10 sites. Temperature, salinity and oxygen saturation were also measured by multiparametric probe and a visual census for vegetation was performed. Sites close to freshwater inflow were characterized by lower temperature and salinity, and high nitrate, with maxima of 191.05 μM in May 2010 and more than 250 μM in October 2010. Silicates drastically decreased from May 2010 (87.57 μM) to July 2010 (6.15 μM) and increased again in October (74.99 μM). Chl a concentrations were not on average higher than 6 mg m, but peaks of 20 mg m were observed during May 2011 and May 2012. Benthic vegetation wet biomass collected in 2010 was approximately twice that collected in 2012, with a maximum of 27,554 g m and a dominance of macroalgae (70 % in May 2010 and 40 % in August 2010). During period 2010, a simultaneous and drastic decreasing of both mean values of wet biomass and chl a was observed from May to October 2010. During period 2012 a shift of vegetation biomass was shown from May (phytoplankton prevalence) to August 2012, with angiosperm prevalence (more than 30 %). [ABSTRACT FROM AUTHOR]