Groundwater is a vital resource in coastal areas, which are often characterized by high population densities and vulnerability to groundwater quality degradation from various factors. These factors include seawater intrusion, which occurs when saltwater mixes with freshwater due to over-extraction or changes in sea level. Land-use changes, such as urbanization and agriculture, can also degrade groundwater quality by increasing pollution and reducing recharge. Additionally, natural disasters like cyclones and floods can have both positive and negative impacts on groundwater, depending on the severity and duration of the event. This study investigated the impact of Cyclone NIVAR (2020) on groundwater quality in the coastal areas of Thiruvallur district, Tamil Nadu, India. Water samples were collected monthly from 35 locations between January 2020 and January 2021 and analysed for Physico-chemical parameters, cations and anions. Data from the State Ground and Surface Water Resources Data Centre (PWD, Tharamani) were incorporated to compare with historical trends. ArcGIS was used to map the spatial distribution of groundwater quality for pre and post-cyclone scenarios. Results showed that the TDS range decreased from 390–3471 mg/L pre-cyclone to 208–2500 mg/L post-cyclone. Groundwater levels (GWL) also exhibited a substantial increase, rising from a pre-cyclone range of 1.66 m to 10.2 m to −0.39 m to 3.81 m after the cyclone. This elevation suggests significant aquifer recharge from cyclonic rainfall. The study concludes that Cyclone NIVAR led to a substantial increase in groundwater levels, indicating that controlled aquifer recharge could be a viable strategy for sustainable groundwater management in similar coastal regions.