The Muota rises on the Ruosalp, an alp to the north of the Glatten on the border between the cantons of Schwyz and Uri. Initially, it flows in a northerly direction through the tiny Bisistal before turning west to the villages of Muotathal and Ried.
Beyond Ried, the river flows through a narrow defile between the Gibelhorn and Stooshorn, passing under the
Stoosbahn 
funicular that serves the mountain resort of
Stoos 
, as it does so. After leaving this canyon, the river turns north to reach the village of Ibach in the municipality of Schwyz.