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Two mesocosms experiments were conducted in winter 2010 and summer 2011 to examine how increased pCO2 and/or nutrient concentrations potentially perturbate dissolved organic matter dynamics in natural microbial assemblages. The fluorescence signals of protein- and humic-like compounds were used as a proxy for labile and non-labile material, respectively, while the evolution of bacterial populations, chlorophyll a (Chl a) and dissolved organic carbon (DOC) concentrations were used as a proxy for biological activity. For both seasons, the presence of elevated pCO2 did not cause any significant change in the DOC dynamics (p-value that these changes depended on initial microbial populations and the availability of extra nutrient inputs. Based on our results, it is expected that in the future projected coastal scenarios the eutrophication processes will favor the transformations of labile and recalcitrant carbon regardless of changes in pCO2.