The internal organization of plankton communities plays a key role in biogeochemical cycles and functioning of aquatic ecosystems. In this study, the structure of a marine plankton community (including both unicellular and multicellular organisms) was inferred applying an ecological network approach to species abundances observed weekly at the Long-Term Ecological Research site MareChiara (LTER-MC) in the Gulf of Naples (Tyrrhenian Sea, Mediterranean Sea) in the summers 2002-2009. Two distinct conditions, characterized by different combination of salinity and chlorophyll values, alternated at the site: one influenced by coastal waters, herein named ‘green’, and the other reflecting more offshore conditions, named ‘blue’. The green and blue ‘phases’ showed different keystone biological elements: namely, large diatoms and small-sized flagellates, respectively. Several correlations among species belonging to different trophic groups were found in both phases (connectance ~ 0.30). In the green phase, several links between phytoplankton and mesozooplankton and within the latter were detected, suggesting matter flow from microbes up to carnivorous zooplankton. A microbial-loop-like sub-web, including hetero-mixotrophic dinoflagellates and ciliates, was present in the green phase, but it was relatively more important in the blue phase. The latter observation suggests a more intense cycling of matter at the microbial trophic-level in the blue phase. These results show that different modes of ecological organization can emerge from relatively small changes in the composition of aquatic communities coping with environmental variability. This highlights a significant plasticity in the internal structure of plankton webs, which should be taken into account in predictions of the potential effects of climatic oscillations on aquatic ecosystems and biogeochemical cycles therein.