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Located in the central part of the country, it reaches both the south and north coasts of the island. It borders the Strait of Wetar to the north, the districts of Baucau and Viqueque to the east, the Timor Sea to the south and the districts of Manufahi, Aileu and Dili to the west. It has a population of 42,742 inhabitants (Census 2010) and an area of 1,706 km2. The longest river in Timor-Leste, the Laclo river, reaches the sea near Manatuto, between the Ponta de Subaio and Lanessana bay.

The climate in Manatuto District is tropical, with rainfall and a wet season which differs between the northern and southern regions. The temperature in the dry season varies between a minimum of 18ºC and a maximum of 32ºC. In the north the minimum is 20ºC and the maximum is 32ºC.