The River Musizi is located in the western part of Uganda. It starts from the hills, northwest of the town of Mubende in Mubende district, central Uganda. It flows in a north-western direction to empty into Lake Albert, on the border between Uganda and the Democratic Republic of the Congo.

The source of River Muzizi is located in Mubende district, River Muzizi enters Lake Albert at Ndaiga, in Kibaale district, on its course north-westwards, the river traverses or forms the borders of the following districts: Mubende district, kyegegwa district, Kibaale district, kyenjojo district, kabarole district, Kibaale district and Ntoroko district. At its source, the altitude is approximately 1,300 meters (4,300 ft). At its point of entry into Lake Albert, the altitude is approximately 650 meters (2,130 ft)

The length of river Muzizi is approximately 120 kilometers (75 mi) from source to end.