Fluid polarity shifts initiate and amplify preferential flow in clay-rich media.

Preferential flow governs fluid and solute transport across scales from micropores to regional watersheds, yet it is commonly attributed to static pore-structure heterogeneity. Here, we show that fluid polarity can actively reorganize pore networks and amplify preferential flow in kaolinite-rich clay media. In permeation experiments, replacing water with a low-polar hydrofluoroether triggers early breakthrough (~0.4 d) and permeability up to ~62.7× higher than predicted by standard relative permeability functions at only 18.8% low-polar saturation. Multiscale imaging and porosimetry show a transition from unimodal microporosity to connected pore-fracture bimodal architectures. Interfacial measurements indicate that low-polar fluids weaken interparticle electrostatic repulsion and thereby reorganize pore space by reducing ineffective pores and activating latent connectivity. Guided by the cross-scale mechanistic chain, we establish a one-parameter relationship linking interfacial forces to ineffective porosity and integrate it into a coupled framework that reproduces preferential path development and permeability evolution across 21 clay-rich media and 24 fluids. These findings advance a cross-scale framework for polarity-driven transport dynamics and provide a basis for incorporating fluid polarity into predictive subsurface transport models in shallow clay-rich environments.