Solid state nanochannels modified with supramolecular architectures are a new and interesting class of stimuli-responsive nanofluidic element. Their fundamental understanding requires describing the behavior of soft-materials in confined geometries and its responses to changes in solution conditions. Here, a nanochannel modified with a polyelectrolyte brush is studied with a molecular theory that incorporates the conformational behavior of the polymers, electrostatic, van der Waals, and repulsive interactions coupled with the ability of the polymer segments to regulate their charge through acid-base equilibrium. The theory predicts pH-dependent ionic conductivity in excellent agreement with experimental observations. The polymer chains undergo large conformational changes triggered by variations in the outer solution environment and the conductivity of the device is shown to be controlled by the charge state of the polymer. The degree of polymer charge is largely affected by charge regulation and nanoconfinement effects. The molecular calculations show that the apparent pK(a) inside the pore departs from that in solution when increasing the curvature of the nanochannel.