In the North Aegean, the geometry complexity and the high variability in the prevailing strong winds conduce in the development and evolution of special circulation characteristics in the coastal areas, as well as in several cyclonic and anticyclonic systems in the open sea. Additionally, the water masses exchange with the less dense Black Sea affects almost the entire N. Aegean Sea region. The implementation of a 3-dimensional, hydrodynamic, hybrid-coordinate model (based on the HYCOM code, https://hycom.org), at a high resolution of 1/50° in the North Aegean (hereafter NAEG-HYCOM) is employed to examine the physical oceanography of the region. Particularly, this study focuses on the understanding of the processes that influence the transport and fate of Black Sea Waters (BSW) through the Northern Aegean Sea and the development of a methodology to parameterize and simulate the coupling of the Aegean and Black Seas through the Dardanelles Strait.