It is very important to develop a rehabilitation plan for the watersheds that have been degraded because of increased development activities and high urbanization. Identifying the most vulnerable parts of a watershed is challenging and can be done if water quality in the river was determined in different sections from the upstream to the downstream of a watershed. In this study, we delineated the Skudai River watershed into 25 sub-watersheds using ArcGIS technique. Later, we identified tributaries in each sub-watershed. The subwatersheds were grouped into three main categories, i.e. natural, semi-urban, and urban subwatersheds depending on land use patterns. Water quality samples were collected at different tributaries from all three categories of sub-watersheds. The paper presents water quality analysis results. The Skudai River (natural part) was classified into natural sub-watershed as this sub-watershed was dominated with natural forest. The Senai and Kempas rivers were classified into sub-urban watersheds while Melana and Danga rivers were classified into urban watersheds. The water quality index (WQI) for the Skudai River (Natural) was 95.2 and falls in Class I category, i.e. clean. The Senai River had WQI of 84.5 and Class II category, i.e. slightly polluted. However, Kempas River which was also in the sub-urban watershed had calculated WQI of 54.5, in Class III and polluted. Melana River was also polluted river with WQI of 68.8 (Class III). The Danga River was also polluted river with WQI value as 55.2. Water quality in the direction of flow in the Skudai River was deteriorating because of some local pollutants entry on the way
