Selective proton (H+) permeation through the atomically thin lattice of graphene and other 2D materials offers new opportunities for energy conversion/storage and novel separations. Practical applications necessitate scalable synthesis via approaches such as chemical vapor deposition (CVD) that inevitably introduce sub-nanometer defects, grain boundaries and wrinkles, and understanding their influence on H+ transport and selectivity for large-area membranes is imperative but remains elusive. Using electrically driven transport of H+ and potassium ions (K+) we probe the influence of intrinsic sub-nanometer defects in monolayer CVD graphene across length-scales for the first time. At the micron scale, the areal H+ conductance of CVD graphene (∼4.5–6 mS cm−2) is comparable to that of mechanically exfoliated graphene indicating similarly high crystalline quality within a domain, albeit with K+ transport (∼1.7 mS cm−2). However, centimeter-scale Nafion|graphene|Nafion devices with several graphene domains show areal H+ conductance of ∼339 mS cm−2 and K+ conductance of ∼23.8 mS cm−2 (graphene conductance for H+ is ∼1735 mS cm−2 and for K+ it is ∼47.6 mS cm−2). Using a mathematical-transport-model and Nafion filled polycarbonate track etched supports, we systematically deconstruct the observed orders of magnitude increase in H+ conductance for centimeter-scale CVD graphene. The mitigation of defects (>1.6 nm), wrinkles and tears via interfacial polymerization results in a conductance of ∼1848 mS cm−2 for H+ and ∼75.3 mS cm−2 for K+ (H+/K+ selectivity of ∼24.5) via intrinsic sub-nanometer proton selective defects in CVD graphene. We demonstrate atomically thin membranes with significantly higher ionic selectivity than state-of-the-art proton exchange membranes while maintaining comparable H+ conductance. Our work provides a new framework to assess H+ conductance and selectivity of large-area 2D membranes and highlights the role of intrinsic sub-nanometer proton selective defects for practical applications.