Nyköpingsån is one of two rivers to flow into the harbour of Nyköping, the other being Kilaån that winds through the southwestern part of the municipality eastwards from Kolmården.

The highest source of the river is the small lake of Svartsjön in Hallsberg Municipality, Örebro County at 187 metres (614 ft) above sea level.

[3] The innermost source and furthest western part is Norra Dovrasjön also in Hallsberg Municipality at a somewhat lower elevation.

[3] Although a shorter and lower route, it also leads into the lake of Tisnaren in Östergötland County in the north of Finspång Municipality.

At the innermost part, the gap between two lakes in the drainage area of Nyköpingsån and the one of Vättern and Motala ström is just above 110 metres (360 ft).