Heterogeneity exerts an important control on solute transport pathways in any subsurface environment, including aquitards where diffusion is the dominant transport mechanism. Direct‐push (D‐P) electrical conductivity (EC) logging has recently enabled high‐resolution hydrostratigraphic characterization of predominantly coarse‐grained sediments in low‐salinity aquifers. In this paper, we apply D‐P EC logging to characterize the spatial variability of physical and chemical properties in a clay‐rich aquitard that has known vertical contrasts in pore water salinity. The D‐P EC logging was conducted to a maximum depth of 17.5 m below ground (BG). Results obtained from 22 D‐P EC logs across a 140‐ × 80‐m field site were compared with pore water chemistry data from squeezed core samples (n= 21) and piezometers (n= 6) to reveal complex spatial variations in pore water salinity ranging from <5000 to ∼90,000 μS/cm. The EC distributions appear to be controlled by nonuniform salt fluxes from the unsaturated zone to the water table and subsequent downward diffusion. Detailed D‐P EC logging also revealed the presence of a single discontinuous sand lens located between 9.4 and 15.9 m BG that may have important controls on solute transport pathways. The only limitation with using this method in very fine‐grained sediments is that depths of tool penetration may be considerably less than those currently achievable in sand and silt deposits.