The country is located on the East African plateau, lying mostly between latitudes 4°N and 2°S (a small area is north of 4°), and longitudes 29° and 35°E. It averages about 1,100 metres (3,609 ft) above sea level, and this slopes very steadily downwards to the Sudanese Plain to the north. However, much of the south is poorly drained, while the centre is dominated by Lake Kyoga, which is also surrounded by extensive marshy areas. Uganda lies almost completely within the Nile basin. The Victoria Nile drains from the lake into Lake Kyoga and thence into Lake Albert on the Congolese border. It then runs northwards into South Sudan. One small area on the eastern edge of Uganda is drained by the Turkwel River, part of the internal drainage basin of Lake Turkana.

Lake Kyoga serves as a rough boundary between Bantu speakers in the south and Nilotic and Central Sudanic language speakers in the north. Despite the division between north and south in political affairs, this linguistic boundary runs roughly from northwest to southeast, near the course of the Nile. However, many Ugandans live among people who speak different languages, especially in rural areas. Some sources describe regional variation in terms of physical characteristics, clothing, bodily adornment, and mannerisms, but others claim that those differences are disappearing.

Although generally equatorial, the climate is not uniform as the altitude modifies the climate. Southern Uganda is wetter with rain generally spread throughout the year. At Entebbe on the northern shore of Lake Victoria, most rain falls from March to June and in the November/December period. Further to the north a dry season gradually emerges; at Gulu about 120 km from the South Sudanese border, November to February is much drier than the rest of the year.

The northeastern Karamoja region has the driest climate and is prone to droughts in some years. Rwenzori, a snowy peaked mountainous region on the southwest border with Congo (DRC), receives heavy rain all year round and is the source of the Nile. The south of the country is heavily influenced by one of the world’s biggest lakes, Lake Victoria, which contains many islands. It prevents temperatures from varying significantly and increases cloudiness and rainfall. Most important cities are located in the south, near Lake Victoria, including the capital Kampala and the nearby city of Entebbe.

Although landlocked, Uganda contains many large lakes; besides Lake Victoria and Lake Kyoga, there are Lake Albert, Lake Edward and the smaller Lake George.