The Flossach rises near the village of Gerum, northwest of Türkheim at an elevation of 588 m (1,929 ft).

It flows in a northwesterly direction through a broad valley, formed during the last glacial times.

The 14.5 km (9.0 mi) long Weissbach flows parallel to the Flossach in the same valley.

Approximately 900 m (3,000 ft) below the mouth of the brook Wörth, the Flossach divides into two branches.

The main Flossach branch flows through the towns of Tussenhausen and Zaisertshofen; the other branch (called the Lettenbach or Lehnbachof) flows through Mattsiesmühle (north of Mattsies) and along the Mindelheim-Mattsies airfield.