<p>Deltaic regions of India are highly vulnerable to seawater intrusion due to the proximity to the sea, reduced river discharge, and intensive groundwater extraction. This study was carried out in the Pennar delta of southern India to evaluate seawater intrusion in shallow and deep aquifers using hydrogeochemical indicators and stable isotopes (<i>δ</i>¹⁸O and <i>δ</i>²H). Rainfall variation emerged as the primary factor influencing groundwater fluctuations. Key salinity indicators (Na/Cl, Mg²⁺/Ca²⁺, Ca²⁺/HCO₃⁻ + SO₄²⁻), Na–Cl facies, hydrochemical facies evolution diagrams (HFE-D), and stable isotopes confirm multiple salinization mechanisms. Coastal sites in Vidavaluru and Muthukuru mandals show strong salinity, reflected by elevated Cl⁻/alkalinity ratios and low total alkalinity (TA)/total hardness (TH) values. Shallow wells near Krishnapatnam and Katepalli indicate direct seawater intrusion linked to aquaculture, with isotopic enrichment from evaporated seawater. Deep wells of the inland delta show extreme salinity with a meteoric isotopic composition, suggesting paleo-salinity or upconing of highly saline water. Deep wells near the seacoast at Isakapalli have relatively low total dissolved solids (TDS) but elevated Mg²⁺/Ca²⁺ and seawater-like isotopic values, suggesting early-stage salinization influenced by evaporation, likely from adjacent saltpans. The shallow wells at Nelaturu reflect saline surface water seepage from an ash pond. Thus, groundwater salinity arises from direct seawater intrusion, evaporative enrichment, paleo-salinity, and anthropogenic contamination. Preventing leakage from ash ponds and regulating extraction in coastal zones are vital to protecting freshwater resources from seawater intrusion.</p>