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Differentiation of the plankton food web structure was studied during the 2003–2008 period, in situations when the system of the northern Adriatic Sea, one of the most productive area in the Mediterranean, switched from low nutrient to higher nutrient regime. The biomass distribution between autotrophs, bacteria, protozoans and metazoans showed that within the upper part of the water column the microbial food web was developed during the stratification period (May–September) in oligotrophic conditions, with a larger heterotrophic/autotrophic (H/A) ratio in the western (1.4–1.7) than in the eastern part (1.2–1.5). Classical food web patterns (H/A 0.3–0.7) were observed when additional nutrient supply by freshwater (stratification period) or/and by mixing throughout the water column (November–March) occurred. However, while the stratification period with freshets (originated from the Po River outflow) was characterized by an increased biomass of autotrophs and heterotrophs, there was a reduction of biomasses during the mixing period, indicating increased carbon export from the area. In the bottom layer heterotrophs were not able to use the excess of autotrophic production, hence probably a part of autotrophs sank to the sediments fuelling benthic communities. Moreover, recurrently higher metazoans than protozoans biomass ratios suggested the occurrence of herbivorous and microbial grazing modes of metazoans.