The first surprise: boats to Comino do not leave from Valletta. They leave from Malta’s north and east coasts, and the harbour that suits you depends on where you sleep and on the slot of your lagoon pass.
On St Paul’s Bay, in the north. Both 6-hour cruises leave from here: to Comino (9:00, 9:30, 10:00, 11:00 and 16:30; €40) and Gozo and Comino (9:00 to 12:00; €45), plus the hop-on ferry at 10:40. A 90-minute crossing to Comino. If you stay in Buġibba, Qawra or St Paul’s Bay, this is your harbour.
Opposite Valletta, across Marsamxett harbour. The hop-on ferry (10:00; €36), the open-bar catamaran (10:30; €89) and the schooner (€75, with pickup at the island’s main hotels) leave from here. If you sleep in Sliema, St Julian’s or Valletta, it is the natural harbour.
Malta’s northern tip, where the Gozo ferry leaves. It is the closest harbour to Comino and the scheduled launches to the lagoon leave from here, but we have not verified that service’s times or prices and do not publish them. If you go independently, check the boat is on blcomino.com’s official list of authorised vessels.
Departure from Buġibba at 9:00 with a 90-minute crossing: you reach Comino around 10:30, well inside the pass’s morning slot (08:00–13:00). The 16:30 departure: afternoon slot (13:30–17:30), with little margin. The 10:00 Sliema ferry, if you go to Gozo first, drops you on Comino already in the afternoon slot. Book the pass after choosing the boat, not before.