Managed aquifer recharge (MAR) is being practiced for improving groundwater storage and quality. The objective of the present study is to access the impact of the check dams as a method of MAR on the spatial and temporal dynamics in groundwater quality. The present study was carried out in the Arani-Kortallaiyar River basin, located north of Chennai, southern India where several check dams have been constructed. This area is also a part of the multi-layered coastal aquifer with an upper and a lower aquifer, which are affected by seawater intrusion since 1969. Due to the high rate of pumping from the lower aquifer for agriculture and public water supply, the extent of seawater intrusion is higher in the lower aquifer than the upper aquifer. Groundwater modelling carried out for the period until 2030 indicated that rejuvenating the unmaintained surface water bodies in the study area such as lakes, ponds etc., increasing the recharge through check dams and decreasing groundwater pumping will reduce the seawater intrusion from 14 km to about 8 km. Simulated results also indicated that with 10% increase in recharge and with 10% reduction from the current pumping rate, the groundwater levels will increase up to 3 m in the upper aquifer and up to 6 m in the lower aquifer. As an extreme scenario, the effect of 10% decrease in rainfall and 10% decrease in pumping was also predicted. This indicated that even though there is decrease in rainfall, by reducing the groundwater pumping, the groundwater levels will increase by about 1 m in both the upper and lower aquifers. The groundwater quality also improves as the chloride concentration decreases by about 1400 mg/l in the upper aquifer and about 950 mg/l in the lower aquifer at the end of 2030. Thus, check dams constructed along the non-perennial rivers help in reviving contaminated aquifers and improving the groundwater quantity and quality.