The Malagarasi River is a river of southeastern Burundi and northwestern Tanzania, flowing through Kigoma Region. It is the second longest river in the country, at 475 kilometres and with a basin area of 130,000 square kilometres, the Malagarasi has the largest watershed of all of the rivers flowing into Lake Tanganyika The source of the river.
The first 80 kilometres of the river form the international boundary between Tanzania and Burundi. Several tributaries from the Burundi highlands join its right bank. After the confluence with the Lumpungu River, the Malagarasi enters Tanzania.