Vertical mixing and stratification are among the most important physical processes controlling nutrient dynamics, the dominant category of primary producers and consequently the dominant types of food web, and are therefore important for the assessment of the marine ecosystem's response to global climate change. This study showed consistent short-term cyclic successions of the plankton food web types, governed by the dynamics of water column stability changes, occurring in generally oligotrophic, phosphate deficient surface waters of the open middle Adriatic Sea. The biogeochemical nitrogen cycle appeared as a key driving force responsible for the food web structure changes. The ‘herbivorous food web’ dominated during the nitrate-rich mixed water column period (winter) and gradually changed to ‘multivorous food web’ where large phytoplankton still constitute a significant fraction of phytoplankton. This intermediate type of food web lasted for a short time and quickly changed to the typical ‘microbial food web’, which then dominated during the stratified water column period (summer) and was characterised by a large proportion of picoplankton size-fraction organisms in total plankton biomass and production. Furthermore, at the very end of summer, the high bacterial carbon flux through the ‘microbial loop’ was established. The succession of food web types affects the mechanisms of bacterial control in a way that ‘bottom up’ control dominated during the mixed water column period and ‘top-down’ control prevailed during the stratified period. Since the ongoing global warming is expected to change water column stability dynamics and thereby significantly affect the supply of nutrients in surface waters, this study helps to understand the possible direction of changes in the plankton food webs of the Adriatic Sea, and consequent changes in marine nitrogen and carbon biogeochemical cycles.