The Archaeological Museum of Agios Nikolaos is located north of the lake, at 74 Paleologou Street, a short distance from the town centre.

The museum was established in 1970 and houses a rich collection of archaeological finds from Lassithi Prefecture.

In the eight rooms of the museum are displayed archaeological treasures dating from the Neolithic (6000 BC) and Minoan (3000 BC) period to Roman times (1st-2nd century AD).

The most impressive of all the exhibits in the museum is the skull of a young athlete from the Roman cemetery in the Potamos area, near Agios Nikolaos. The skull dates from the 1st century AD and is crowned with a golden diadem of olive leaves.

In the mouth of the dead youth was a silver coin from the city of Polyrrhenia in west Crete, dated to the reign of the Roman Emperor Tiberius. According to ancient tradition, the coin was to pay Charon, the ferryman who carried souls to the netherworld (Hades) across the Acherusian Lake.