Lipsi has a safe natural harbour which is approximately the same size as the port of Lavrion  and its design is such that it can manage more traffic than it currently receives. Port and maritime activities are covered by the Lipsi Harbour Station, which can assist vessels from abroad.

The port is divided into three areas:

1. Tourist area for the docking of public passenger ships and vessels 
2. Recreational Boats and Yachts area for the mooring of private pleasure craft (motor and sailing boats)
3. Commercial area for the docking of any kind of cargo boat, for supplies of water, fuel and other goods.