Nanopores play a decisive role in different technologies from oil production, separation, and sensing to drug delivery or catalysis and energy conversion. In recent years, abilities to functionalize nanopores have advanced significantly. Thereby, nanopores functionalized with polyelectrolytes or responsive polymers show fascinating transport properties, such as gated or gradually controlled ionic permselectivity. Nonetheless, understanding the influence of external parameters such as ion type or concentration on nanopore performance, and thus on the mentioned applications, remains a challenge but is crucial for applications. In this work, the effect of different counterions on the wetting and ionic transport in poly(2-(methacryloyloxy)ethyltrimethylammonium chloride)-functionalized silica mesopores (pore diameter <10 nm) was experimentally and theoretically investigated. Static contact angles covered a range from 45 to almost 90° by exclusively changing the counterion. Ionic pore accessibility was also strongly dependent on the counterion present and was found to gradually change from accessible pores up to complete, pH-independent ion exclusion. On the basis of molecular theory calculations, these experimental observations were rationalized on the basis of ion binding between the [2-(methacryloyloxy)ethyl]trimethylammonium chloride monomers and the counterions. In addition, the theoretical framework provided a nanoscopic view into the molecular organization inside the pores, showing a strong dependence of ion concentration and ion distribution profiles along the pore radius in dependence of the present ions. The obtained insights on the role of counterion type and ion binding in nanopores are expected to have direct impact on the above-mentioned applications.