The town directly borders Sengkang to the south and shares riverine boundaries with the planning area of Seletar to the west and Pasir Ris to the east. Bounding the town to the north and north-east is the Straits of Johor, with Coney Island included as a part of the Punggol planning area.

Punggol is divided into 7 subzones, namely, Matilda District, Waterway West District, Northshore District, Punggol Point District, Canal District, Waterway East District and Crescent District