The extraction of mountain salt from the saline waters is the basic livelihood of the Ba'kelalan communities of Sarawak. The current integrated approach is the first attempt to study the sources and geochemical processes of the saline groundwaters in this mountain region. Hence, in this study, saline groundwater samples from five existing wells in different seasons were analysed for hydrochemical parameters and multi-isotope composition (δ18O, δD, δ34S, δ11B and δ37Cl). The significant increase in TDS, EC and salinity was due to seasonal variation and fluctuation in water level based on hourly, daily and monthly observations. The geochemical ratios and the statistical techniques revealed that the salinity was due to the dissolution of marine evaporites as a dominant process, coupled with other factors such as water-rock interaction, ion exchange and sulphate reduction. From the isotopic signatures, it was inferred that the origin of saline groundwater was from the intense dissolution of marine evaporites such as halite dissolution and oxidation of -sulphide (pyrite). 2D electrical resistivity and seismic refraction methods were used to identify the lithological variations, depth of potential sources of saline groundwater, and the subsurface structures. It was inferred the probability of a conductive zone at a depth of 1–14 m, from which the saline groundwater plume migrates towards the perched aquifer. The presence of subsurface faults facilitated the movement of hypersaline groundwater from the saturated zone to the surface. The outcome of the study will support the dependent community to enhance their commercial salt production.