The port of Scrabster lies a mile and a half west of the estuary of the River Thurso. It has a deep water harbour in the shelter of Holborn Head. The harbour includes a berth for the MV Hamnavoe, a roll-on/roll-off ferry linking the mainland with Stromness on Orkney, and is Orkney's main connection to Great Britain.
Scrabster Harbour is an important port for the Scottish fishing industry, and is now the 2nd largest whitefish harbour in Scotland. A large fishmart is held at Scrabster and the local lifeboat is stationed there too.
- The Northlink ferry (MV Hamnavoe) leaves from Scrabster regularly for Stromness in Orkney.
- In summer months, Smyril Line operated a weekly service to the Faroe Islands, but this was discontinued in 2008 and awaits any replacement.
- Smyril Line operated a service from Scrabster to Iceland in 2008.