The history of Agios Nikolaos is marked by its harbour in the Ammoudi area, which is still the commercial port of the town.
This site was chosen for a major harbour in East Crete, because the islets of Agioi Pantes before it offered better defences against possible attackers and good shelter from the northwesterlies, which can blow quite strongly.
In the Venetian period, the harbour of Agios Nikolaos had a capacity of 25 galleys, a fairly significant number for the time, and served the needs of East Crete. Today, you can travel from here to Piraeus and various islands.
The two islets of Agioi Pantes (All Saints), the natural breakwaters of the harbour, now shelter a few Cretan Wild Goats (agrimia), a species at risk of extinction.