Background: The impact of watershed land-use on surface water quality, especially in urbanized areas, has been investigated in numerous studies in developed countries, however, the issue is one of the under researched areas in developing cities of Africa. To study the impact of watershed land-use on surface water quality, we used the main land use types of the Kebena watershed from aerial photograph and collected river water samples during the dry and wet seasons for two consecutive years at different points from the river course. We calculated the share of each land use using ArcGIS and tested the water quality during each season. The variations in water quality parameters relating to the different land use types of the sub-watersheds were analyzed using ANOVA. Results: Kebena watershed is mainly covered by 39.14% forest, 32.51% built-up area and 27.25% cultivated land. At sub-catchment level, Denkaka, (agriculture dominated) sub-catchment with 44.90 % cultivated land, Little Kebena, (forest dominated) sub-catchment, with 60.87% forest cover and Ginfle (urban dominated) sub-catchment with 90.44% built-up area were identified. The variations in water quality parameters relating to the different land use types of Kebena watershed revealed the significantly high seasonal relationship between the concentration of the water quality indicators during the dry season at (P<0.001, P<0.05). Furthermore, there is a strong positive relationship between the urban and forest dominated sub-catchments and water quality indicators during both the wet and dry seasons than agriculture dominated sub-catchment.Conclusion: Integrating watershed planning with land use planning, therefore, becomes one of the vital tools to address water quality problems in a holistic manner to further prioritize restoration and protection strategies for specific sub-catchments. Thus, in the urban dominated sub-catchment, relocating riverfront communities, providing a well-designed sewage system, applying appropriate storm water management schemes, are some of the important measures while providing wide river buffers with various vegetation cover are necessary to minimize pollutants influx to the river from the agriculture dominated sub-catchment. Furthermore, in the forested sub-catchment, applying preventive measures to retain and enhance connectivity of the existing natural green spaces through open space planning, development and management schemes is crucial.