Transport properties and stability of ionic species in films of conducting polymers polypyrrole (PPy) and poly(3,4-ethylenedioxythiophene) (PEDT) were examined by electrochemical quartz crystal microgravimetry (EQCM) experiments. The mobility of ions in these polymers were greatly affected by the mode of polymerization with which the polymer film was prepared, as well as by the structure of the ions. When the conducting polymers were doped with macrocyclic anions, phthalocyanine and porphyrin derivatized with sulfonate anionic groups, these anions were not expelled from the PPy or PEDT films by extensive potential cycles. Heteropolytungstate ions have partial mobility in the polymers and were expelled by negative potential sweeps applied to the films that were formed by electropolymerization at a constant potential or constant current. Polymer films formed with alternating potential programs showed drastically diminished permeability to anions. By forming a polymer film with cyclic potential sweeps or square wave potentials, it was possible to examine transport of other ions without complications due to the transport of the initial dopant ions.