The transport of weak acid/base molecules through ultrathin films of polyelectrolyte complex formed by the multilayering method was measured by electrochemical means. The net flux of probe molecule through multilayers is a linear combination of all forms in which that probe is found. Neutral molecules are able to traverse the membrane faster because they rely on nonspecific hopping, whereas charged molecules require extrinsically charged sites, which are doped into the multilayer by external salt. Control over probe charge by external pH is thus an effective way to influence net membrane transport. Flux was simulated by Monte Carlo methods and by analytical expressions, which showed that the pH-dependent component of flux was essentially mirrored by the solution titration curve of the weak acid. In situ attenuated total internal reflection Fourier transform IR measurements revealed that multilayer probe concentration was independent of both the solution salt concentration and state of ionization.