South Sudan lies between latitudes 3° and 13°N, and longitudes 24° and 36°E. It is covered in tropical forest, swamps, and grassland. The White Nile passes through the country, passing by Juba.

Fauna, flora, and mycobiota
South Sudan's protected areas host the second largest wildlife migration in the world. Surveys have revealed that Boma National Park, west of the Ethiopian border, as well as the Sudd wetland and Southern National Park near the border with Congo, provided habitat for large populations of hartebeest, kob, topi, buffalo, elephants, giraffes, and lions. South Sudan's forest reserves also provided habitat for bongo, giant forest hogs, Red River Hogs, forest elephants, chimpanzees, and forest monkeys. Surveys begun in 2005 by WCS in partnership with the semi-autonomous government of Southern Sudan revealed that significant, though diminished wildlife populations still exist, and that, astonishingly, the huge migration of 1.3 million antelopes in the southeast is substantially intact.

Habitats in the country include grasslands, high-altitude plateaus and escarpments, wooded and grassy savannas, floodplains, and wetlands. Associated wildlife species include the endemic white-eared kob and Nile Lechwe, as well as elephants, giraffes, Common Eland, Giant Eland, oryx, lions, African Wild Dogs, Cape Buffalo, and topi (locally called tiang). Little is known about the white-eared kob and tiang, whose magnificent migrations were legendary before the civil war. The Boma-Jonglei Landscape region encompasses Boma National Park, broad pasturelands and floodplains, Bandingilo National Park, and the Sudd, a vast area of swamp and seasonally flooded grasslands that includes the Zeraf Wildlife Reserve.

Little is known of the fungi of South Sudan. A list of fungi in Sudan was prepared by S.A.J. Tarr and published by the then Commonwealth Mycological Institute (Kew, Surrey, UK) in 1955. The list, of 383 species in 175 genera, included all fungi observed within the then boundaries of the country. Many of those records relate to what is now South Sudan. Most of the species recorded were associated with diseases of crops. The true number of species of fungi occurring in South Sudan is likely to be much higher. Nothing is known of the conservation status of fungi in South Sudan although, like animals and plants, they are likely to be affected by climate change, pollution, and other threats.

In 2006, President Kiir announced that his government would do everything possible to protect and propagate South Sudanese fauna and flora, and seek to reduce the effects of wildfires, waste dumping, and water pollution. The environment is threatened by the development of the economy and infrastructure.

According to the WWF, several ecoregions extend across South Sudan: the East Sudanian savanna, Northern Congolian forest-savanna mosaic, Saharan flooded grasslands (Sudd), Sahelian Acacia savanna, East African montane forests, and the Northern Acacia-Commiphora bushlands and thickets.

South Sudan has a population of around 6 million and a predominantly rural, subsistence economy. This region has been negatively affected by war for all but 10 years of the independence period (1956), resulting in serious neglect, lack of infrastructure development, and major destruction and displacement. More than 2 million people have died, and more than 4 million are internally displaced persons or became refugees as a result of the civil war and war-related impacts. Here the South Sudanese practice mainly indigenous traditional beliefs, although some practice Christianity, as a result of Christian missionary efforts. The south also contains many tribal groups and uses many more languages than the north. The Dinka (pop. est. more than 1 million) is the largest of the many Sub-Saharan tribes of South Sudan. Along with the Shilluk and the Nuer, they are among the Nilotic tribes. The Acholi and Lotuhu live in the extreme south, extending into Uganda.