[1] The Malše originates in the territory of Sandl in the Gratzen Mountains at an elevation of 985 m (3,232 ft), on the slope of the Viehberg mountain, and flows to České Budějovice, where it enters the Vltava River at an elevation of 384 m (1,260 ft).

[2][3] The longest tributaries of the Malše are:[4] The most notable settlement on the river is the city of České Budějovice.

In Austria, the river flows past the territories of Sandl, Windhaag bei Freistadt and Leopoldschlag, then turns north into the hinterland of the Czech Republic.

The river then flows through the municipal territories of Dolní Dvořiště, Bujanov, Kaplice, Soběnov, Svatý Jan nad Malší, Velešín, Římov, Doudleby, Plav, Vidov, Roudné and České Budějovice.

It serves as a drinking water reservoir for České Budějovice and the surrounding area.