The Submarine Groundwater Discharge (SGD) in the coastal aquifer was first estimated in the Andaman Islands of India. The SGD plays an essential role in maintaining the ecological balance of nearshore systems and supporting the region’s economy. A hydrological modelling approach was employed to assess the temporal distribution of groundwater discharge, particularly in coastal zones. The significance of South Andaman’s coastal regions as vital natural resources and understanding the complex interactions between coastal hydrological processes and marine ecosystems is essential. This study utilizes an integrated hydrological modelling technique to evaluate SGD along the South Andaman shoreline. The results, obtained under steady-state conditions, indicate that the current daily average SGD is approximately 0.0034 m3/day per meter of shoreline. However, the findings highlight that SGD values are significantly influenced by factors such as climate change, variations in coastal aquifer groundwater levels, recharge rates, and sea level rise. Furthermore, the study highlights a significant exponential correlation between groundwater levels and SGD in the coastal unconfined aquifer, underscoring the dynamic interplay between groundwater and the sea. The study insights contribute to a better understanding of SGD mechanisms and their essential for sustainable water resource management and coastal ecosystem conservation in this region.