We describe transport among different regions of the ocean by flow networks, giving a discrete and robust representation of the fluid advection dynamics. We use this approach to study the surface circulation in the Mediterranean Sea. Using network-theory tools we analyze flow networks in the sea domain to gain insights into transport problem. Local and global features of the networks are extracted from many numerical experiments to give a time averaged description of the system. Classical concepts like dispersion, mixing and connectivity are finally related to a set of network-like objects contributing to build a "dictionary" between network measures and physical quantities in the ocean.