Beginning in the highlands of Algonquin Park they flow southwesterly, uniting in Bracebridge. They then continue to flow into Lake Muskoka. The Lower Muskoka subwatershed receives the inflow from the North and South Branches as well as Lake Joseph, Lake Rosseau, and Gull and Silver Lakes in Gravenhurst.
It rises in the highlands of Algonquin Park and flows southwest through a number of lakes including; Lake Muskoka, Lake Joseph, Lake Rosseau, Lake of Bays
which empty into Georgian Bay south of Parry Sound by way of the Moon and Musquash Rivers.
Tributaries include the:
Communities on the river include:
The name "Muskoka" comes from the name of a chief of the Ojibwa in this region, "Mesqua Ukee" (Miskwaa-aki: Red Earth).