The river rises in the Lausitzer Bergland (Upper Lusatia) at an altitude of 317 m above sea level. NN on the east flank of the 396 meter high summit, a secondary summit of the Hochstein.
The source is about 1.5 kilometers south of the town of Kindisch, which belongs to Elstra. From there the Black Elster first flows in a northerly direction through Elstra, Kamenz, Milstrich and Wittichenau. From Hoyerswerda it flows west to Elsterheide. In the further course, after 63 kilometers, it passes the Saxon-Brandenburg border. Immediately after the border, the Black Elster crosses the Koschen Canal between Groß- and Kleinkoschen in a waterway junction. Then it flows through Senftenberg and Ruhland to Lauchhammer. There, with the Schraden, which covers around 15,000 hectares, it reaches the Pulsnitz estuary.
After the Black Elster has passed the seven kilometer narrowest point of the Breslau-Magdeburg glacial valley near Elsterwerda, it swings in a northwesterly direction and flows in the Elbe-Elster lowland through the cities of Bad Liebenwerda, Herzberg and Jessen, among others. It flows out at river kilometer 198.5 at an altitude of 69 m above sea level. NN near the municipality of Elster (Elbe) in the Elbe.