Cyclic voltammetry was applied to investigate the permselective properties of electrode-supported ion-exchange polymer films intended for use in future molecular-scale spectroscopic studies of bipolar membranes. The ability of thin ionomer film assemblies to exclude mobile ions charged similarly to the polymer (co-ions) and accumulate ions charged opposite to the polymer (counterions) was scrutinized through use of the diffusible redox probe molecules [Ru(NH3)6]3+ and [IrCl6]2−. With the anion exchange membrane (AEM) phase supported on a carbon disk electrode, bipolar junctions formed by addition of a cation exchange membrane (CEM) overlayer demonstrated high selectivity toward redox ion extraction and exclusion. For junctions formed using a Fumion® AEM phase and a Nafion® overlayer, [IrCl6]2− ions exchanged into Fumion® prior to Nafion® overcoating remained entrapped and the Fumion® excluded [Ru(NH3)6]3+ ions for durability testing periods of more than 20 h under conditions of interest for eventual in situ spectral measurements. Experiments with the Sustainion® anion exchange ionomer uncovered evidence for [IrCl6]2− ion coordination to pendant imidazolium groups on the polymer. A cyclic voltammetric method for estimation of the effective diffusion coefficient and equilibrium extraction constant for redox active probe ions within inert, uniform density electrode-supported thin films was applied to examine charge transport mechanisms.