Changes in the land cover are determined by a complex set of interactions between environmental and socio-economic factors. Classified satellite images for the years 2005 and 2009 show substantial changes in different land covers. These changes are considered to reflect natural expansion and contraction in the area of vegetation types, as well as human induced land use changes. Major changes have been observed in the Mau Complex due to human encroachment. Other critical watersheds affected are the montane ecosystem of Mt. Elgon, Mt. Rwenzori and the Ethiopian Highlands.
Land cover change by sub-basins indicates the decline of forest areas and increase of cultivated land in almost all the subbasins.
| Name | Class | % change 2005 – 2009 | Change (km2) 2005 – 2009 |
| Forest | 4 | -18.1 | -46803.29 |
| Shrubs | 6 | -0.7 | -6605.15 |
| Grasslands | 7 | 2.0 | 3609.61 |
| Cultivated/Agriculture | 8 | 5.9 | 40239.18 |
| Wetlands | 9 | -2.9 | -1458.22 |
| Bare areas | 12 | 1.3 | 12517.51 |
| Water bodies | 13 | -1.3 | -1261.41 |