Lake Toba lies in the northern part of Barisan Mountain Range, which is volcanic and traverses Sumatra Island from northwest to southeast as its backbone. The laketrough is surrounded by precipitous cliffs 400 - 1,200 m high. Based on the topographic feature and the wide distribution of volcanic ejecta around the lake, some geologists and volcanologists have considered it to be a giant caldera or cauldron.

The water surface of Lake Toba is 905 m above sea level and about 1,100 km² wide. The total area of the lake, including the areas of Samosir and Paradapur Islands, amounts to 1,780 km². The mountains around the lake are called Batak Highlands. The only draining river from Lake Toba, the Asahan, flows southeastwards dissecting the gentle slopes of the pyroclastic plateau.