Ion transport through porous substrates is ubiquitous in biological and synthetic materials, and fundamental for chemical separation, drug delivery and bio-sensing. Contemporary imaging techniques for simultaneously characterizing topography and ion transport through porous substrates are limited in range and resolution. In this paper, we demonstrate 'surface-tracked scanning ion conductance microscopy' as a technique to image topography of a porous substrate and simultaneously measure voltage-driven transmembrane ion transport. This technique uses the principles of 'shear-force tracking' to image the surface of a polycarbonate track-etch membrane, and chronoamperometry to reconstruct topography-correlated transmembrane ion transport through the membrane at different transmembrane potentials. Spatial transmembrane transport through individual pores is modeled using Goldman-Hodgkin-Katz (GHK) theory to examine the effects of shear-force modulation on magnitude of transmembrane currents recorded with a nanopipette. The modeled transmembrane current through the porous membrane is compared with experimental behavior, and discrepancies between predicted values and measured data are outlined. The proposed surface-tracked imaging mode allows for rapid assessment (approximately 7 s/μm) of interfacial processes at the nanoscale and addresses a bottleneck for stable, large-area characterization of porous substrates using scanning ion conductance microscopy.