Coastal aquifers are vital water sources for over a billion people worldwide, providing fresh water to areas that are often affected by seawater intrusion and groundwater depletion due to anthropogenic and environmental changes. Groundwater flow modelling is a powerful tool for understanding flow dynamics and managing water resources sustainably. This is the first effort to conduct a numerical simulation modelling for the Ramanathapuram coastal aquifer, located in the southeastern part of Tamil Nadu, to investigate the groundwater flow patterns in a shallow coastal aquifer to optimise freshwater management and mitigate seawater intrusion. The study region has complex geological formations and a semi-arid climate, and is facing challenges such as over-extraction and salinity intrusion. The finite difference approach with the Visual MODFLOW package was utilised to simulate the groundwater flow and calibration and validation over a ten-year period (2014–2023). Key hydrogeological parameters, including hydraulic conductivity (K) and specific storage (Ss), were determined based on field data from 23 observation wells. The model was discretised into 11,788 grid cells, and boundary conditions such as constant head from the Bay of Bengal and natural rainfall recharge were applied. The calibration and validation outcomes reveal a high degree of alignment between measured and modelled groundwater levels, affirming the reliability of the simulation. Qualitative analysis using head equipotential maps and time series data reveals significant variations in groundwater levels, with the northwest region exhibiting high groundwater storage while the eastern region shows lower levels due to over-extraction. Flow velocity maps provide insights into groundwater movement directions, which is critical for understanding recharge and discharge zones. In addition, mass balance calculations indicate the distribution of water inputs and outputs, further validating the model’s reliability. This study demonstrates the effectiveness of numerical modelling in managing coastal groundwater resources and provides a robust tool for predicting future water dynamics and informing sustainable water management strategies. The findings underscore the importance of detailed hydrological models in addressing groundwater challenges in coastal regions, offering valuable insights to manage water resources sustainably.