While the water impermeable constraint has been conventionally adopted for analyzing the transport phenomena at the interface of electrolyte/nanoporous medium, non-negligible water-permeance through the medium results in significant effect on ion and particle transportation. In this work, a rigorous theoretical and experimental analysis of the water-permeance effect were conducted based on a fully-coupled analytical/numerical method and micro/nanofluidic experiments. The regime diagram with three distinctive types of concentration boundary layers (ion depletion, ion accumulation, and intermediate) near the ion exchange nanoporous medium was proposed depending on the medium’s permselectivity and the water-permeance represented by an absorbing parameter. Moreover, the critical absorbing parameters which divide the regimes were analytically obtained so that the bidirectional motion of particles were demonstrated only by altering the water-permeance without external stimuli. Conclusively, the presenting analysis of non-negligible water-permeance would be a substantial fundamental of transport phenomena at the interface of the ion exchange medium and electrolyte, especially useful for the tunable particle/ion manipulations in intermediate Peclet number environment.