The purpose of this study is to understand the impact of coastal groundwater over-exploitation on the variations in submarine groundwater discharge (SGD) flux rate and seawater exchange flux across the seabed. As a case study, numerical modelling techniques were applied to a complex multi-aquifer system located north of Chennai, India, which has been affected since the mid-1970s by overexploitation and seawater intrusion. Because of the relatively high hydraulic conductivity, the model shows a higher amount of seawater inflow in the central part of the region. From 2000 to 2012, the movement of seawater has increased from 17,000 m3/day to 24,500 m3/day due to groundwater overexploitation from the semi-confined aquifer. However, the quantum of flux from the sea to the aquifer has been reduced from the year 2006 due to the termination of pumping from a well field supplying a part of the city’s water supply. Model simulations show that fresh groundwater of 43,312 m3/day and saltwater of 43,815 m3/day will be discharged to the aquifer by the end of 2030. In addition to the prevailing condition, various management scenarios were also predicted to prevent the degradation of groundwater quality due to seawater intrusion. By adopting managed aquifer recharge methods, saltwater intrusion (rate of 4408 m3/day) can be reduced and SGD (rate of 22414 m3/day) rate increased. Findings from this study are expected to enhance the understanding of SGD and freshwater budget in coastal areas and in creating integrated coastal management plans.