The temporal dynamics of microphytoplankton, microzooplankton and mesozooplankton were monitored over 37 months in the Adriatic Sea in order to identify alterations in the plankton structures, which can lead to, or enhance the production of macro-aggregates, that affected the entire northern basin in summers 2000 and 2002, and to assess any negative effects of mucilage on plankton temporal patterns. Samples were collected monthly, from June 1999 to July 2002, on three transects at 9 stations across the northern and central Adriatic Sea. Besides the high year-to-year variations in abundances and taxonomical composition, plankton communities only showed a clear seasonal succession during 2001, when since April a grazing food web developed and was able to control large sized phytoplankton increase. In spring-summer 2000 and 2002 consumer abundances remained quite low and the dominant mesozooplankton summer species (Penilia avirostris) did not reach its usual summer maximum. The lack of an efficient top control was more evident on the northernmost transect, where generally grazing food web prevails over the microbial one. A large part of the microphytoplankton blooms, although not particularly intense, was exported to the bottom in the particulate phase, where it was processed by bacteria, enhancing the production of refractory dissolved material.