| Drainage Basin | 1994 (Area km2) | % | 2008 (Area km2) | % | % Change |
| Albert Nile | 1736.3 | 6.21 | 1255.2 | 4.71 | 27.7 |
| Aswa | 3028.0 | 10.83 | 2168.9 | 8.24 | 28.4 |
| Kidepo | 168.1 | 0.60 | 197.2 | 0.74 | −17.3 |
| Lake Albert | 2838.6 | 10.15 | 2421.7 | 9.20 | 14.6 |
| Lake Edward | 1671.1 | 5.97 | 1096.3 | 4.16 | 34.4 |
| Lake Kyoga | 15008.3 | 53.67 | 11028.5 | 41.92 | 26.5 |
| Lake Victoria | 7167.6 | 25.63 | 3310.2 | 12.58 | 53.8 |
| Victoria Nile | 5786.3 | 20.69 | 4829.4 | 18.35 | 16.5 |