The Kirnitzsch, also called the Kirnscht or Kirnsch in the local dialect, rises in the Lusatian Highlands in Bohemia west of the village of Studánka (German Schönborn) and flows westwards through the town of Krásná Lípa (Schönlinde).

Behind the village of Kyjov [cs; de] (Khaa, part of Krásná Lípa) it wends its way along narrow ravines through the sandstone rocks of Bohemian Switzerland.

Further downstream the Kirnitzsch is first impounded at the Obere Schleuse ("Upper Lock") so that boating can take place on the stream.

At the end of the Kirnitzsch Gorge (Kirnitzschklamm) used to stand the houses of the border village of Zadní Jetřichovice [cz; de; it] (Hinterdittersbach) and the settlement of Křinice (Kirnscht).

From here the Kirnitzsch flows through Saxon Switzerland, where it is impounded again at the Niedere Schleuse ("Lower Lock").