Groundwater in coastal alluvial deltas is highly vulnerable to lateral and vertical solute transport as it is connected through complex network of tidal creeks, local sea level rise and anthropogenic stresses, particularly under changing climatic conditions and rising population density. This study investigates how complex lithostratigraphic heterogeneity, surface water–groundwater interactions, and coastal salinity processes control the vertical and lateral groundwater vulnerability of the Indian Sundarbans, an active alluvial delta and UNESCO World Heritage Site. An integrated methodological approach combining multi-criteria decision-making (MCDM), stable isotopic signatures (δ18O and δ2H), and solute chemistry was employed. Results indicate that inland groundwater (>100 km) is vulnerable to both vertical and lateral pollution (salinity: 1.4–2.3 PSU; NO3−: 0.1–19.8 mg/L), driven by discontinuous lithological structures and hydraulic connectivity with tide-dominated creeks (salinity: 10.4–23.5 PSU). Conversely, nearshore groundwater is primarily affected by saline water intrusion, which overshadows vertical contamination signatures, plausibly influenced by population-driven hydraulic imbalances (819 persons/km2) in surface water–groundwater interactions. Isotopic analysis reveals subtle spatial variability between inland zones (δ18O: −1.33 to −1.47‰; d-excess: −2.03 to 4.5‰) and nearshore zones (δ18O: −1.42 to −1.47‰; d-excess: −2.01 to 5.8‰), indicating predominantly meteoric recharge with variable evaporative influence and localized salinization. Therefore, these integrated approaches provide an effective decision-support framework for protecting deltaic groundwater resources from agricultural pollution and saline water encroachment, aligned with SDG-6.