South Sudan is situated in northern Africa bordering Central African Republic, Chad, Democratic Republic of the Congo, Ethiopia, Kenya and Uganda. It is dominated by the River Nile and its arms. The terrain is generally flat plains, broken by several mountain ranges; the highest mountain is Mount Kinyeti Imatong, near the border with Uganda. Rich mineral resources are available in South Sudan including: petroleum, natural gas, gold, silver, chromite, asbestos, manganese, gypsum, mica, zinc, iron, lead, uranium, copper, kaolin, cobalt, granite, nickel and tin.There is concern over soil erosion. The amount of rainfall surges towards the south where there are swamps and rain forests. Sudan's rainy season lasts for up to six months June to November in the south. The dry regions are plagued by sand storms, known as haboob, which can completely block out the sun.

In the northern and western semi desert areas, people rely on the scant rainfall for basic agriculture and many are nomadic, traveling with their herds of sheep and camels. Nearer the River Nile, there are well-irrigated farms growing cash crops. Agricultural expansion, both public and private, has proceeded without conservation measures. The consequences have manifested themselves in the form of deforestation, soil desiccation, and the lowering of soil fertility and the water table. The nation's wildlife is threatened by hunting.

The climate is tropical with warm/hot temperatures, average temperature of 37 ◦C in February, and 29 ◦C in July with scarce rainfall. The monthly rainfall varies between 2 (January) and 127 mm (October).