[1] The Stropnice originates in the territory of Moorbad Harbach in the Gratzen Mountains at an elevation of 860 m (2,820 ft) and flows to Doudleby, where it enters the Malše River at an elevation of 412 m (1,352 ft).

[2][3] The longest tributaries of the Stropnice are:[4] There are no significant towns on the river.

The river flows through the municipal territories of Moorbad Harbach, Horní Stropnice, Nové Hrady, Petříkov, Olešnice, Jílovice, Borovany, Trhové Sviny, Ostrolovský Újezd, Strážkovice, Komařice, Římov and Doudleby.

The middle course of the river flows through the Třeboň Basin, which is known for abundance of fishponds.

[5] The Stropnice is occasionally suitable for river tourism, but only in spring after heavy rains or melting snow.