Basin ground water has not been adequately studied and so, information in this area is still scanty. An inventory of trans-boundary aquifers was obtained from International Groundwater Resources Assessment Centre (IGRAC), an organization which facilitates and promotes international sharing of information and knowledge required for sustainable groundwater resources development and management worldwide. The layer provided by IGRAC, identifies twelve (12) trans-boundary aquifers within the Nile basin, the largest being the Nubian Sandstone Aquifer System covering an area of about 567,344 Km2 in the Nile basin.
| FID | Aquifer Name | Countries | Total Aquifer Area (Km2) | Aquifer Area in the Nile Basin (Km2) | % area within Nile Basin |
| 1 | Mount Elgon Aquifer | Uganda, Kenya | 5,398.32 | 4,579.49 | 85% |
| 2 | Gedaref | Ethiopia, Sudan | 57,830.51 | 51,369.10 | 89% |
| 3 | Mereb | Ethiopia, Eritrea | 38,752.68 | 27,210.24 | 70% |
| 4 | Rift Aquifer | Kenya, Tanzania | 21,145.08 | 1,780.24 | 8% |
| 5 | Kagera Aquifer | Tanzania, Rwanda, Uganda | 5,778.95 | 5,218.10 | 90% |
| 6 | Baggara Basin | Central African Republic, South Sudan, Sudan | 239,876.71 | 196,127.11 | 82% |
| 7 | Coastal Aquifer Basin | Egypt, Israel, Palestinian Territory | 23,338.14 | 11.72521552 | 0% |
| 8 | Karoo-Carbonate | Central African Republic, Congo, South Sudan | 604,596.15 | 120,947.00 | 20% |
| 9 | Tanganyika | Burundi, Democratic Republic of the Congo, Tanzania | 184,594.89 | 2,279.49 | 1% |
| 10 | Nubian Sandstone Aquifer System (NSAS) | Chad, Egypt, Libya, Sudan | 2,892,867.48 | 567,344.75 | 20% |
| 11 | Aquifere du Rift | Democratic Republic of the Congo, South Sudan, Uganda | 44,632.12 | 30,023.07 | 67% |
| 12 | Sudd Basin | Ethiopia, Kenya, South Sudan | 370,647.62 | 324,287.18 | 87% |