In this study, the impact of change in land use and land cover (LULC) on runoff estimation in the Kidangoor watershed was assessed using the SCS-CN technique. Recent flood-like natural disasters in Kerala are thought to be driven by changes in rainfall patterns and LULC. The accurate calculation of runoff from watersheds is urgently needed. In ArcGIS 10.5, the supervised classification approach is used to classify satellite images from 2000, 2011, 2013, and 2017. Similarly, the Inverse Distance Weighted (IDW) technique is used to produce spatial distribution maps of rainfall for each antecedent moisture condition (AMC). The runoff maps were generated by superimposing the distributed rainfall, LULC, and Hydrological Soil Group (HSG) maps. It was observed that the built-up area expanded by 168% between 2000 and 2017, whereas other classes decreased by 10–23%. However, compared to 2000, both with and without a change in LULC, runoff generation increased by just 31%, and 27% in 2017. The SCS-CN technique for runoff estimation indicates that the change in LULC in the Kidangoor watershed is insignificant. Thus, this study will help land use planners and decision-makers in limiting the potential damage from flooding when it comes to flood management techniques.