Salinity, both in soil and water, is a ubiquitous problem in coastal Bangladesh, particularly in the southwest. Salinity varies at the local scale (5–10 m), but the relative roles of land use and surface geology on salinity variation in near-surface (< 5 m) groundwater are not fully understood. Surface geology, land use and salinity in near-surface (ca. 3 m) groundwater at two small sites (each 0.05 km2) were explored in the southwest coastal region of Bangladesh. The sediments in the near-surface at both sites are fine and hydrometer analyses of cored samples indicate the dominance of silty clay (70%) along with very fine sand (5%), sandy clay (15%) and clay (10%) materials. Salinity variation in near-surface groundwater tends to follow land use rather than surface geology at the scale of our investigations. The study provides evidence of the influence of land use on the near-surface salinity variation and indicates the importance of land-use planning in salinity management in coastal areas.