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This study evaluated groundwater quality of the coastal aquifer in Nagapattinam district with intensive agricultural activities in the southern part of India. Chemical components such as pH, EC, TDS, major cations and anions were used to identify seawater intrusion. Fifty-two groundwater samples were collected from dug and bore wells in this region during summer and monsoon seasons, 2011. EC, TDS, Na and Cl were higher in summer than in monsoon. The correlation and two-way-joining cluster analyses clearly show that groundwater quality is mainly controlled by seawater intrusion and other anthropogenic sources. Modified Hill–Piper exhibits that most of the samples belong to water contaminated with gypsum sector. The interpretation of Gibbs plot represents the groundwater samples that fall in evaporation and rock weathering zone, and other samples are affiliated to various anthropogenic activities. Based on Na %, SAR, chloride, hardness and Wilcox classification, the groundwater is moderately suitable for agriculture. This region is vulnerable to seawater intrusion during summer due to the severe pumping of groundwater. In groundwater quality maps produced by inverse distance weighting of ArcGIS, some good and medium patches could be used for agriculture to a certain extent. The northern, southern and central parts of the study area fell in poor quality regions because of seawater intrusion and infiltration of irrigation water contaminated with pesticides and fertilizers.