During the SESAME project a study was undertaken in the northern Aegean Sea and simultaneously in the Turkish Straits System (TSS). The composition and the structure of the pelagic food web were examined in order to understand the transfer of phytoplankton production up the food chain in TSS and the Aegean Sea. The results of this study confirm our hypothesis that there is a substantial differentiation within pelagic food web structure and carbon flow from Bosphorus to the Aegean Sea. Ocean acidification has now been widely acknowledged as 'the other CO2 problem' and recognised by a number of countries as an important research priority. Thus, we investigated the impact of ocean acidification (OA) on pelagic food web processes in a coastal area of the Eastern Mediterranean Sea through a series of laboratory experiments. Our findings revealed that the different functional groups of plankton and biological processes presented diverse response to increased CO2 that might have impact on the structure of the pelagic food web of the Mediterranean Sea. Given the potential threat to marine ecosystems and the ensuing impact on human society and economy, OA is arguably the most critical environmental issue that humans will have to face in the immediate future.