Lake Mutanda is located in Kisoro District in south western Uganda, approximately 20 kilometers (12 mi) north of the town of Kisoro, where the district headquarters are located. This location is approximately 454 kilometers (282 mi), by road, south west of Kampala, Uganda’s capital and largest city.

Lake Mutanda is nestled in the foot hills of the Virunga mountain range, at an altitude of 1,800 meters (5,900 ft). The three volcanoes within the range that is partly located in Uganda, namely: Mount Muhabura, Mount Sabinyo and Mount Mgahinga, can be viewed from Lake Mutanda. There are several islands in the Lake. The Lake is drained by the Rutshuru River, which flows northward to Lake Edward.