The Sebnitz rises in the Šluknov Hook in a broad valley between the 608-metre-high Hrazený (Pirsken) and the 593-metre-high Plešný (Plissenberg), 2 kilometres northwest of the village of Brtníky (Zeidler).

The stream flows in a northwesterly direction to Velký Šenov (Groß Schönau), where it swings southwest and follows the valley of Šenov stream (Czech: Šenovský potok), passing between Vilémov (German: Wölmsdorf) and Mikulášovice.

Below these villages the Wölmsdorfer Bach between the hills of Spálený vrch (Hillebrand, 443 m) and the Wolfstein (392.9 m) near Dolina (Franzthal) the stream forms the border between the Czech Republic and the tip of the Sebnitz Forest that throws a salient into Bohemian territory.

After passing the border crossing of Sebnitz-Dolní Poustevna it continues for several hundred metres along the border before flowing through the town of Sebnitz, named after it, as well as the picturesque Sebnitz valley before uniting with the Polenz after 30.8 kilometres (19.1 mi) above Porschdorf to form the Lachsbach.

The most important tributaries of the Sebnitz are the: Since 1995 there has been a cross-border project, the Elbe Lachs, which aims to reintroduce salmon to the Elbe and several of its tributaries, including the Sebnitz.