The Nera rises in the Semenic mountains, the easternmost part of the Banat region, south of the city of Reșița, in the Caraș-Severin County of Romania.

In this section, the Nera receives its left tributary, the Rudăria, and passes next to many villages (Prilipeț, Dalboșeț, Moceriș), until it reaches Șopotu-Nou, where it sharply turns to the northwest, still curving around the Semenic mountains.

In the border section, the Nera flows through the depression of Bela Crkva (Belocrkvanska kotlina; Cyrillic: Белоцркванска котлина), and settlements on the Romanian side include Lescovița, Zlatița and Socol, while on the Serbian side there is only one village on the river itself, Kusić, with several settlements in the vicinity of the river: Kaluđerovo, the town of Bela Crkva, Vračev Gaj and Banatska Palanka.

In the final section, the Nera is 20 to 40 metres (66 to 131 ft) wide with varying depths, and as the riverbed is made mostly of gravel, it spills over in series of limans, filled with murky waters.

After the filling of the artificial Lake Đerdap, as a result of the Iron Gate I Hydroelectric Power Station which was finished in 1972, the mouth of the river into the Danube was flooded.