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South Sudan is situated in northern Africa. It borders the countries of Central African Republic, Chad, Democratic Republic of the Congo, Ethiopia, Kenya and Uganda. It is dominated by the River Nile and its tributaries. The terrain is generally flat plains, broken by several mountain ranges; the highest mountain is Mount Kinyeti Imatong, near the border with Uganda.

The amount of rainfall increases towards the south where there are swamps and rain forest. 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.

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. 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. As of 2001, twenty-one mammal species and nine bird species are endangered, as well as two types of plants. Endangered species include: the waldrapp, northern white rhinoceros, tora hartebeest and the slender-horned gazelle. In May 2007, it was announced that hundreds of wild elephants had been located on a previously unknown, treeless island in the Sudd swampland region of southern Sudan. The exact location being kept secret to protect the animals from poachers.