We investigated the short-term changes in the shallow water table for the highly urbanized Cochin city of Kerala, India. The monthly water table observed at 97 Well locations for 16 months was used to generate a monthly water table fluctuation map and a seasonal recharge map. The majority of the coastal plains of the study area shows low recharge depths, while the eastern midland part shows moderate to high recharge. The quantification of the recharge affirms the proportionality of the recharge depths to precipitation. Seasonal recharge maps illustrated a significant recharge during the southwest monsoon period. Further, the monthly groundwater discharge flux rates using Darcy’s tool suggest a high discharge from east to west. The mapped seepage velocity signifies a higher seepage rate from the midland portion of the study area. The spatial distribution patterns of total dissolved solids (TDS), electrical conductivity (EC), and pH concentrations display flush-out patterns that connect the freshwater availability to recharge from rainfall. Quality parameters are better in the midland region, indicating higher recharge in the midland than in the coastal lowland region and discharge from the midland to the lowland. Our study summarizes that the dynamics of the aquifer system in the midland region are more active due to laterite formation and steeper hydraulic gradients. The majority of enriched groundwater from the midland was draining out immediately after the monsoon period, which leads to a severe water crisis during the non-monsoon period. The study emphasizes the need to implement appropriate aquifer management based on the prevailing aquifer dynamics for sustainable groundwater resources.