The harbours or ports of Crete Island are located at Heraklion, Chania, Agios Nikolaos, Rethymno, Sitia and Kastelli-Kissamos.
Direct daily ferries link Piraeus (Athens) to Heraklion, Chania and Rethymno.
Pireas to Heraklion: Ships depart every evening around 8.00 or 8.30 (times vary a little depending on the season) and arrive very early morning (5.00 or 6.00 am). Sailing take about 9 hours on standard ferries (ANEK Lines), 6 hours on the highspeed Knossos Palace and Festos Palace of the Minoan Lines fleet.
Pireas to Rethymno: Also served by ANEK Lines overnight ferries.
Pireas to Chania: the ANEK Lines overnight ferries take 9 hours, whereas the Highspeed catamaran of Hellenic Seaways takes 4.5 hours and sails at daytime.
Three weekly ferries are travelling from Heraklion to Santorini and from Sitia to Piraeus, passing by Agios Nikolaos and, one a week, by Milos.
There are three weekly ferries from Heraklion to Thessaloniki via Santorini Greece. Twice a week, via Paros, Tinos and Skiathos and one a week via Naxos, Syros and Volos.
A ferry leaves from Crete twice per week and stops along the way at Milos, Agios Nikolaos and Sitia in Crete, before it sails to Karpathos, and Rodes. From Rodes it returns back the reverse route before it reaches Piraeus.
Two weekly ferries are linking Kastelli-Kissamos(45 km west of Chania) to Antikythira, Kythira, Kalamata and Githio.Timetables are rather erratic.
From April to October there are boats from Santorini (and other Cycladic islands) to Heraklion and Agios Nikolaos.
IMPORTANT NOTE: The ferries sail when the weather is considered suitable and stable conditions are predicted. If the weather is bad, sailings will be cancelled (not often - but there are a few such days every year), and you should be accommodated on the next available sailing.