We investigated the effect of external pH, ionic strength, and applied voltage to control the transport of ions through porous PCTE/Au/acid thiol membranes with pore radii of 4.0-5.9 nm. Electroless gold was deposited on the inside surfaces of the nanopores of the membrane. The thiols 11-mercaptoundecanoic acid (HSC10H20COOH) and 3-mercapto-1-propanesulfonic acid (HSC3H6SO3H) were used to form self-assembled monolayers (SAMs) on the gold surfaces of the pores. The ionic permeant through the pores of the membranes was the organic ion benzene sulfonate (BS). The transport of benzene sulfonate in porous membranes modified with SAMs of the HSC10H20COOH weak acid thiol was highly affected by external variation of the pH; the BS flux could be changed by a factor of 100. However, transport of benzene sulfonate in membranes modified with SAMs of the HSC3H6SO3H strong acid thiol was influenced less by external pH than transport in membranes modified with SAMs of the HSC10H20COOH weak acid thiol. Increasing the ionic strength of the bulk solution caused the flux of benzene sulfonate to increase due to the decrease of the Debye length. Application of a voltage to the membrane has a significant influence on the benzene sulfonate flux through the porous membrane. Controlling the pH and the applied potential can lead to flux changes as large as a factor of 170.