Vatakara is located at and has an average elevation of . It is situated about 49 km to the north of Kozhikode City, approximately 44 km to the south of Kannur City, and adjacent to Mahé. The town lies by the side of a river variously called the Moorad river, the Kuttiady river, or Kottakkal river. The town's position relative to this river led to it being called Vadakkekara (north bank), later contracted to Vatakara. Towards the east, near the panchayats of Nadapuram and Kuttiady, Vadakara borders the Wayanad district along the Western Ghats section. In the west, like many of the towns in Kerala, Vatakara is flanked by the Arabian Sea. The Kuttiyadi river meets the sea to the south of Vatakara, forming small islands and sandbars near the river mouth.