The hydrologic regime of the Nile River, in particular the discharge regime, is distinctly influenced by the south and eastern highlands precipitation patterns. The hydrology of the Nile is mainly characterized and influenced by high variations in climate and altitude/topography which have a great bearing on flow magnitudes and patterns in the different parts of the basin. The Nile receives its flow from a network of various hydraulic systems, draining the Ethiopian Plateau and the Equatorial Lake Plateau. The network within the basin is of diverse hydrological processes, e.g. tributaries ad streams, wetlands, open water, man-made infrastructures. The Atlas also identifies and presents the water towers of the basin, as the high altitude area (Rwenzori Mountains in western Uganda, Mount Elgon, and the Ethiopian highlands) with registered rainfall in excess of 1,500 mm, they also usually lose less water to evapotranspiration because temperatures are lower.

Presentation of the hydrology of the Nile in this Atlas focused on key stations within the sub-basins of the Nile starting from downstream to upstream; Main Nile, Tekeze Atbara, Blue Nile, Baro Akobo Sobat, White Nile, Bahr el Jebel, Bahr el Ghazal, Lake Albert, Victoria Nile, and ends with Lake Victoria sub-basin. There are also swamps and wetlands in the Nile basin which play and influence the hydrology of the Nile mainly the Sudd, Bahr el Ghazal swamps, and the Machar marshes.

The Ethiopian highlands through the main tributaries (the Blue Nile, Atbara River, Baro-Akobo) are contributing most of the annual flow to the Nile (85%), but its contribution is highly seasonal – highest flows in four months (July – October). The discharges of the Equatorial watersheds into the White Nile are of low magnitude compared to the Ethiopian highlands. However the Equatorial sub-basins contribute more consistent and steady yearround flow. The Nile River course north of Atbara in Sudan receives no tributary and insignificant rainfall contribution. Thereafter, the Nile River flows through dry areas featured by extended desert, storage and the hydrology is dominated by management for multiple uses (irrigation, hydropower, navigation, tourism, etc.) – infrastructures and regulations influence the downstream flow. Further downstream, the Nile discharge into the Mediterranean Sea through its two branches in Egypt (Rosetta and Damietta).

Since the early years of the 20th century, records have been kept of the discharge at key stations of the Nile and its main tributaries. However, due to the fact that the stations records were for different time spans, they can be used to provide a good picture of the seasonal variation and quantify the relative contribution of the respective tributaries to the total Nile flow. The mean annual flow at Dongola station (immediate station upstream Aswan) is about 72 BCM. Inter-annual variability is very high for the long-term annual yield of the Blue Nile and Atbara rivers. While Atbara contributes an average flow of 11.4 BCM, the Blue Nile considered as the major Nile River yields an average of 50 BCM at Ed Deim station (spare its Dinder and Rahad downstream tributaries). Further upstream, the flow at Malakal averages 31 BCM (at the outlet of Baro-Akobo-Sobat, Bahr El Jebel, Bahr El Ghazal sub-basins), compared to an averages of 32 BCM at Mongola (upstream station of Bahr El Jebel sub-basin), which is close to the outflow from Lake Victoria averages 33 BCM. With average annual flow at Gambella of about 11.4 BCM, the Sudd outflow can be computed as 17 BCM. The outflow from the Bahr El Jebel varies little throughout the year because of the regulatory effect of swamps and lagoons of the Sudd region, about half of its water is lost in evaporation (or transpiration through plants), and seepage. Also, the flow duration curve depicts storage characteristics of the Southern stations (e.g. Malakal) compared to the Eastern tributaries.