AbstractIntertidal aquifers are hotspots of biogeochemical cycling where nutrients and contaminants are processed prior to discharge to the ocean. The nature of the dynamic subsurface mixing zone is a critical control on mitigating reactions. Simulation of density‐dependent, variably saturated flow and salt transport incorporating realistic representations of aquifer heterogeneity was conducted within a Monte Carlo framework to investigate influence of nonuniform permeability on intertidal groundwater flow and salt transport dynamics. Results show that heterogeneity coupled with tides creates transient preferential flow paths within the intertidal zone, evolving multiple circulation cells and fingering‐type salinity distributions. Due to heterogeneity, strain‐dominated (intense mixing) and vorticity‐dominated (low mixing) flow regions coexist at small spatial scales, and their spatial extent reaches peaks at high tide and low tide. Such topological characteristics reveal complex tempo‐spatial mixing patterns for intertidal flow with localized areas of high and low mixing intensities, which have implications for intertidal biogeochemical processing.