In 2014, it was reported that hydrated protons are able to traverse nominally pristine monolayer graphene (and hexagonal boron nitride, h-BN) films under ambient conditions. This “intrinsic proton conductivity” of the one-atom-thick crystals, with proposed through-plane conduction, challenged the notion that graphene is impermeable to atoms, ions and molecules. More recent evidence points to a defect-facilitated transport mechanism, analogous to transport through conventional ion-selective membranes based on graphene and h-BN. To clarify the nature of proton transmission through graphene, local ion-flux imaging is performed herein on graphene|Nafion membranes using a new “electrochemical ion (proton) pump cell” mode of scanning electrochemical cell microscopy (SECCM). Targeting regions of the graphene|Nafion membranes that are free from visible macroscopic defects (e.g., cracks, holes etc.), and assessing hundreds to thousands of different sites across the graphene surfaces in a typical experiment, most of the graphene membrane is impermeable to proton transport, with transmission typically occurring at only ≈20 – 60 localized sites across a ≈0.003 mm2 area of membrane (>5000 measurements, total). When localized proton transport occurs, it can be a highly dynamic process, with new transmission sites “opening” and a small number of sites “closing” under an applied electric field, on the seconds timescale. Applying a simple equivalent circuit model of ion-transport through a cylindrical nanopore, the local transmission sites are estimated to possess dimensions (radii) on the (sub)nanometer-scale, implying that rare atomic defects are responsible for proton conductance through monolayer graphene. Overall, this work reinforces SECCM as a premier tool for the structure−property mapping of microscopically complex (electro)materials, with the new configuration reported herein opening up exciting new possibilities in functional membrane characterization, as well as any other application where reactive ion-flux is a highly localized phenomenon, e.g., for diagnosing failure mechanisms in protective surface coatings.