Prioritisation of sub-watersheds (SWs) is becoming increasingly important in the conservation of natural resources, particularly in watershed planning. In this study, sub-watershed for the Neyyar basin was prioritised using three methods: morphometric analysis, principal component analysis (PCA) and hypsometric analysis. Morphometric analysis and hypsometric analysis were carried out using remote sensing (RS) and geographic information system (GIS) techniques, while PCA was performed for dimensionality reduction of morphometric parameters. The watershed was divided into 11 sub-watersheds (SW1–SW11), and each sub-watershed was given priority. To rank and prioritise SWs, 15 morphometric parameters were selected from the quantitative measures of morphometric analysis, including linear, relief, and areal. PCA was used to rank and prioritise SWs based on three highly correlated morphometric parameters. The hypsometric integral (HI) values were determined using the elevation relief ratio approach, and HI values were utilised to prioritise SWs. For both methods, such as morphometric analysis and PCA, a higher priority has been given to SW1. Using hypsometric analysis, higher priorities have been assigned to SW1, SW7, SW8, SW9, SW10 and SW11. The most common SWs that belong to the same priority of SWs and have a high correlation between them among the three methods are SW1, SW2, and SW5.The results of this analysis indicate that SW1 is a common high priority area with a significant risk of soil erosion, runoff and peak discharge. Therefore, decision-makers may utilise the high-priority sub-watershed to guide planning and development, measure conservation efforts and manage the land to prevent.