The objective of this study is to assess the impact of climate change induced rainfall, sea level rise, and urbanization on a fragile coastal aquifer. This study was carried out in one such an aquifer located in Southeast India. Downscaled climate projection was carried out using the regional climate model (RCM) with seven ensembles and the best matching ensemble for the study area has been taken to quantify the rainfall in future. The changes in land use and land cover were estimated using remote sensing techniques, and background information on sea level rise at local and regional scale were investigated. Numerical simulation of groundwater in this isolated coastal aquifer was carried out to understand the responses of the groundwater level to downscaled projected rainfall, sea level rise, expected urbanization, and their combinations until the year 2050. The RCM-projected rainfall shows a decline in the groundwater level and shrinking of the freshwater lens. However, the prediction for change in the groundwater level combined with sea level rise minimizing a decline in the groundwater level. The rapid changes in land use and land cover pattern as inferred by change detection were extended and examined in the aquifer's future characteristics by increasing and decreasing groundwater pumping with RCM-projected rainfall recharge and with sea level rise. The results without considering sea level rise show that the aquifer undergoes degradation even if pumping is reduced by 10%. The simulation with sea level rise shows that the aquifer behaves better in maintaining freshwater lens even with 10% increase in groundwater pumping. Sea level rise prevents the availability of the freshwater lens by reducing groundwater decline caused by the reduced RCM-projected rainfall and predicted groundwater demand. Huge variation and seasonal fluctuation in the volume of outflow to the sea is noticed between north and south. Also, reduced outflow against a range of sea level rise confirms that the sea level rise in the study area will lessen the volume of outflow, will reduce the groundwater decline, and will allow an increase in groundwater level. On the other hand, the shrinking of area will decrease the freshwater volume and occurrence of reduced groundwater gradient against sea level rise will increase the possibility of seawater intrusion to pumping. The present study confirms that even with RCM-projected decrease in rainfall recharge, the increase in the sea level will help to prevent groundwater decline in this aquifer by controlling an elevation of the groundwater level. Meanwhile, it is reducing the volume of freshwater and increasing the possibility of further seawater intrusion. Hence, it is recommended to reduce the groundwater pumping from this aquifer.