The port of Naxos is connected to Athens with regular routes from the ports of Piraeus and Rafina throughout the year. In the summer there are about 4 daily boat departures from Piraeus and 4 from Rafina. During the winter months the frequency is reduced, with at least 1 route per day from Piraeus. The duration of the Piraeus - Naxos journey varies from approximately 3 to 6 hours, while the Rafina - Naxos route lasts from approximately 3 to 7 hours, depending on the ferry.

Also, the port of Naxos is connected to the Cyclades, Crete, the Dodekanisa and the islands of the North Aegean.