The coastal aquifers of Sundarbans, an UNESCO world biodiversity heritage site, are highly vulnerable due to changing climatic conditions, intensification and increasing frequency of extreme climate events and uncontrolled abstraction of groundwater. The exchange of solutes between hydraulically connective shallow and deep aquifers, the seawater intrusion and the role of growing population are poorly understood in the Sundarbans. This study aims to address the solute exchange (Cl−, Sr2+, and salinity) process between surface water and groundwater (SW-GW) at local to regional scale under variable hydraulic head conditions, where annual rainfall is declining and population density is increasing [population 573 (1991) to 819 (2011)/Km2]. Electrical resistivity tomography (ERT) in combination with salinity and δ18O data was used to address the exchange of solutes between SW-GW in a hydraulic continuation. The results revealed that regionally, the Cl− concentration of Sundarbans shows an increasing trend (average 329–351 mg/L) with declining groundwater levels (⁓3 m). Local, depth-dependent study depicting there is a predominant exchange of Sr2+ between shallow depth [D1: 14–25 and D2: 30–50 m below ground level (m bgl)] with seawater (Sr2+: 30–85 μM), which is possibly absent at greater depths (D3:115 and D4: 333 m bgl). The recorded Sr2+ content ranged from 25 to 102 and 16 to 78 μM for shallow depth D1 and D2, respectively, whereas, the Sr2+ concentrations ranged from 1.4 to 6.8 and 1.2 to 5.7 μM for D3 and D4, respectively. The ERT data showed progressively increasing resistivity with increasing depth, similar to high salinity and enriched δ18O at shallow depths and depleted δ18O with low salinity at higher depth reflects the continuous distribution of solutes, which is possibly a result of local downward migration of contaminated shallow brackish water within this physically disconnected zone. The lateral and vertical transportation of solutes in variable hydraulic head conditions would be a measure of drinking water threat in present-day and in imminent future for millions of inhabitants near the coastal area.