The Venetain port acquired its final form in the 16th or 17th century. Then as now, the entrance was dominated by the formidable sea fortress commonly known by the Greek form of its Turkish name Kule ("tower"), which bears out the significance of the area in terms of defence. To the south and west lay the shipyards (arsenali), where the Venetians built and equipped ships for use in war and trade.

Once walled in, the harbour had to be linked to the town - this was achieved mainly by means of two gates, the Porta del Molo (Harbour Gate) and the Gate of the Arsenals (Shipyard Gate), neither of which has survived.

View of the harbour in the early 20th century, showing the Arsenali Gate to the left and the Mole Gate to the right, 1900 - 1905 (G. Gerola, Vikelaia Municipal Library, Heraklion)
The port and the Mole Gate before bombardment in 1898 (Liana Starida Collection)