Brackishwater aquaculture is basically farming in coastal region, and it utilizes the saline water from either sea or estuary or creek. Assessment of hydrogeochemisty of groundwater resources in shrimp farming areas is very much required not only for monitoring the shrimp farming impacts, but also to suggest better management strategies for the long-term sustainability of shrimp farming and integrated water resources management in coastal regions. Watershed-based assessment is ideal as watershed is a geohydrological unit, and it will give the realistic and cumulative effects more precisely. With this background, the present investigation was carried out to evaluate the geochemical process regulating groundwater quality in shrimp farming areas of coastal miniwatersheds of Vellar and Coleroon river, Cuddalore district, Tamil Nadu, along the east coast of India. Representative groundwater (29) samples from shallow aquifer (hand pump and open well) were collected periodically (June 2008, January 2009, April 2009 and July 2009) using the simple random sampling method and analyzed for various water quality parameters viz. pH, TDS, total hardness, alkalinity, cations (Ca+, Mg+, Na+) and anions (Cl−, SO4 −, NO3 −, HCO3 −). The groundwater data indicated that the HCO3 was the dominant ion in the study area with sodium (Na > Ca > Mg) and bicarbonate (HCO3 > Cl > SO4) as the predominant cation and anion, respectively. The large variations in mean and standard deviation of ionic concentration suggest that the water chemistry in the study region was not homogenous and may be influenced by complex sources for the hydrogeochemical processes. The piper trilinear diagram depicts the status of the groundwater quality and also suggests that the cation exchange and mineral dissolution was responsible for this elevated ionic composition at some locations in the study area. The multivariate statistical analysis viz., principal component analysis and cluster analysis clearly elucidated that the groundwater quality in the area is mainly due to natural process and the shrimp farming is not an influencing factor.