In order to better understand the encroachment of seawater into the groundwater system a total 115 groundwater samples were collected in an area of ∼7 km2 in Cox's Bazar paleobeach and its vicinity, from different types of tubewells, which included hand pump fitted bore wells (<50 m depth), moderately deep energized bore wells (50 m–100 m depth) and deep bore wells (>100 m depth) during June 2013. A combined hydro-geochemical indicators, selected trace elements (Sr and B) and in addition to δ18O and δ2H were used in this study. Results show that the high values of EC (202 μS/cm to 6730 μS/cm) and TDS (135 mg/L to 4509 mg/L) are found in groundwater of wells closer to the coast and few wells from the northern and central part of the study area. The cross plot of HCO3/Cl and TDS shows that groundwater along the paleobeach and some isolated areas are saline with TDS > 1000 mg/L, associated with high ratios of Cl/TDS (0.065). The groundwater facies generally evolves from freshwater (Ca-Mg-HCO3) to saline water (Na- Cl) type with an intermediate Ca-Mg-Cl type indicating that the aquifer system interacts with seawater and undergoes cation exchange. Results also reveal that the area affected by marine water intrusion has ionic ratios of Br/Cl (0.0006–0.0021) similar to seawater (0.0015) with some higher values. Groundwaters along the paleobeach and some isolated areas, low ionic ratios of SO4/Cl (0.01–6.53) and Na/Cl (0.20–152.09), relative to marine ratios (0.05 and 0.86 respectively), are also observed. Groundwaters with Seawater Mixing Index >1.0 and TDS >1000 mg/L constitute about 20% of the studied groundwaters and have relatively high δ18O (>- 4.0‰) values and the linear relationships between TDS and most of the ions, including B and Sr, and the chemical signature of the saline plumes (e.g., marine SO4/Cl, Na/Cl and Br/Cl ratios) suggest that mixing processes control the chemical composition of the seawater within the aquifers. However, these geochemical variations also reveal that the quality of potable water has deteriorated to a large extent due to seawater intrusion along the paleobeach, migrating inland toward the heavily groundwater exploited areas from the coast line and may entail various future health hazards. Display omitted •Cox's Bazar paleobeach aquifers are prone to contamination from seawater intrusion.•Hydrogeochemical and isotopic tracers were used to delineate the seawater intrusion in the study area.•Shallow wells (<50 m depth) are contaminated and deep wells (>100 m depth) are safe for drinking water supplies.•Groundwater quality has deteriorated to a large extent along the paleobeach, migrating towards inland.