Compared to the world ocean, the Mediterranean Sea exhibits shorter (=time) and stronger (abrupt changes) responses to environmental stressor and there are closer and faster interactions among the physical and biological processes in the pelagic system, i.e., alterations of the food web (FW) and the biological pump (BP). Furthermore, due to its reduced size, it may be considered as a miniature ocean where in-situ measurements can be carried out relatively easier. Considering these properties and within the context of the “Ocean-Certain project”, two integrated research surveys have been planned to focus specifically on the abrupt changes in the surface current systems over areas which are frequently observed. These areas are the southern and northernmost Aegean Sea and Rhodes gyres in the eastern basin and the Tyrrhenian, NW-Mediterranean, Algerian and Alboran Seas in the western basin. The purpose is to collect real-time data on the physics, biogeochemistry and primary production in the upper layers of the key areas, i.e., straits, channels, shelves, dense water formation sites and deep basins, in order to understand the coupling mechanisms of the changes in surface currents, FW structure and function and the associated BP. Such data set have not been created during the previous cruises in which these key areas had not subject-specific attention. Process-oriented field measurements during the surveys will be carried out in the eastern and western basins. More specifically, the objective is to study the Mediterranean in order to be able to capture the role of thermohaline circulation on the biochemical characteristics of the system. We also expect to study the spreading characteristics of the newly formed deep and intermediate waters in the Aegean and the Adriatic and compare their relative roles on the Mediterranean biogeochemistry and its potential effects on FW and BP. Direct and/or indirect measurements from physics (stratification, thermohaline circulation), to ocean acidification, de-oxygenation, nutrients, export production, respiration/ degradation/ production by microbes, phytoplankton and zooplankton comprise the main themes of the research plan to be carried out. The mesocosm experiment will be designed according to the observed impacts of physical dynamics on the biogeochemistry and connected ecosystem processes.(i.e. changing macro nutrient fluxes to the photic layer etc.). Thus, combining the surveys and the mesocosm experiments will provide us valuable information on the effects of ongoing changes on the FW and BP, as crucially important new data sets which enable us reducing the uncertainties in the models.