The port in Vathi of Samos is located in the part of the large north-eastern natural bay of Samos and is considered as one of the safest natural ports of the arid island of Greece.

The city of Samos is connected by ferry to Piraeus. The liner usually also stops at the island's second port, Karlovasi, which is located on the west side of Samos.

There is also a sparse ferry connection with the rest of the islands of the eastern Aegean and with tourist boats to the port of Kusadasi in Turkey, which is located a short distance to the east.

It is also served by the island's airport located 17 kilometers south of the city.