It has its origin in the eastern slopes of the Yam-Alin, at the confluence of mountain rivers Mata and Seyamni-Makit.

In the upper course the river flows roughly southeastwards within a narrow valley in the area of the Yam-Alin.

[1] After leaving the mountain area, the Nimelen flows first northeastwards across the Nimelen-Chukchagir Lowland and its valley expands.

The river then bends and flows roughly southwards, while it meanders and divides into branches within a wide floodplain with marshes and numerous lakes.

Finally it meets the Amgun 5 kilometres (3.1 mi) to the northeast of imeni Poliny Osipenko, the capital of the Imeni Poliny Osipenko District, 315 kilometres (196 mi) from the Amgun's mouth in the Amur.