Flood is a natural calamity that impacts the lives and property of individuals. Floods result from river overflow, coastal influences, and changes in Land Use Land Cover (LULC). The rapid land cover transformations and changes to natural stream flow pathways are causes of flooding. Changes in LULC along with high rainfall intensity over a short span of time produce more runoff in Kovalam basin. Floods are challenging to regulate; yet, they may be controlled with appropriate flood modelling techniques. This study discusses developing flood modelling for Kovalam basin by integrating GIS with Hydrologic Engineering Centre—Hydrologic Modelling Simulation model (HEC-HMS) and hydraulic Hydrologic Engineering Centre—River Analysis System (HEC-RAS) model. The Kovalam basin was chosen owing to the recurrent floods that occurred in 2015, 2021, and 2023. An extreme rainfall event of 400 mm occurred on 1–2 December 2015 is taken for simulating rainfall runoff process with changing land cover conditions of the years 2014, 2019, and 2024. The flood plain maps were developed for the changing LULC conditions. The maximum flood depth is 1.89 m in year 2014, 1.91 m in 2019, and 1.95 m in 2024 of LULC changes. This study discusses the necessity for developing flood modelling in flood management strategies for reducing flood risks. The proposed study can be implemented in basins with analogous hydrological circumstances.