Fluctuations in groundwater levels along the coast have a significant impact on the extent of saltwater intrusion into freshwater aquifers. This study aims to simulate the groundwater flow and solute transport in the region by using the mSim toolbox in the MATLAB and COMSOL Multiphysics. The investigation is focussed on a micro-basin of Pavanje river located along the west coast of India. The model results are calibrated and validated against the field observations. The results show that the variation of the water table over the year is significant and range from about 3–14 m. There exists a reasonable correlation between the simulated and observed values of groundwater level and salinity. The wells that are most vulnerable to seawater intrusion in the region are identified. The COMSOL model estimated a salinity range of 0–20 mol/m3. Additionally, the model is used to understand the response of coastal aquifer to various stress scenarios. The study reveals that reduced recharge rate with increased pumping has a serious impact on aquifer system.