Bordj Badji Mokhtar is located at an elevation of 401 metres (1,316 ft) in the Tanezrouft, a desolate and mostly flat area in the Sahara Desert.

Unlike most other towns in Saharan Algeria, Bordj Badji Mokhtar is not settled near an oasis but water is available from wells dug 400 metres (1,300 ft) underground.

Occasional showers and thunderstorms do occur from July to September due as the town falls under the far northern edge of influence of the West African Monsoon.

Bordj Badji Mokhtar is very distant from other population centres, but the N6 national highway does connect it to Reggane and Adrar to the north and Timiaouine to the southeast.

The smuggling of drugs, fuel and migrants is an important economic activity in the area, employing the In Khalil border crossing into Mali, about 20 kilometres (12 mi) southeast of the town.