The prefecture of Heraklion is bounded with the prefectures of Rethymno to the west and Lasithi or Lassithi to the east. The valley of farmlands are situated in the central and the northern parts and within the coastline and valleys. The mountains dominate the rest of the prefecture including the south. The main mountains are parts of Ida or Idi Mountains to the west and Asterousia in the south. The prefecture includes the island of Dia to the north.

Within the Heraklion Prefecture's boundaries are a number of significant Neolithic and Minoan settlements, most notably the ancient palace complexes of Knossos and Phaistos. While both archaeological sites evince Neolithic habitation, it is the rich finds of Minoan civilisation, which flourished approximately 2000 to 1600 BC, that command the greatest scholarly attention.

Except for the mountains which receive mild to cool winters unlike northern Greece, the warm to hot Mediterranean climate dominates the prefecture.

• 1991 - 263,868, density: 99.91/km²
• 2001 - 292,482, density: 110.75/km²