The parameters which influence electrochemically facilitated transport of electroinactive ions across conducting electroactive polymer membranes have been investigated. The design of membranes and the materials used as well as transport cells and systems have been addressed to improve selectivity and flux. Polypyrrole-para-toluenesulfonate (PPy-pTS) was compared with the copolymer of pyrrole with 3-carboxy-4-methylpyrrole (PPy/PCMP-pTS) and their different chemistries resulted in different membrane selectivities for ions. Platinum mesh was found to be the most suitable auxiliary electrode material and its placement in the cell chamber(s) facilitated ion incorporation/expulsion at the membrane working electrode. This enhanced the flux of ion transport. The flux can also be further enhanced by narrowing the distance between the membrane working electrode and the platinum mesh auxiliary electrode(s), and/or by stirring to improve the hydrodynamics. An alternative cell design, namely a dual membrane flow through cell, also proved to be more efficient for ion transport. Good connection geometry to the membrane as well as the application of a square wave pulsed potential waveform to the membrane was found to be essential for achieving high and sustainable flux in ion transport.