Microfluidic channels with an embedded ion permselective medium under the application of electric current are commonly used for electrokinetic processes as on-chip ion concentration polarization (ICP) and bioparticle preconcentration to enhance biosensing. Herein, we demonstrate the ability to dynamically control the electrically driven ion transport by integrating individually addressable microvalves. The microvalves are located along a main microchannel that is uniformly coated with a thin layer of an ion-exchange membrane (IEM). The interplay of ionic transport between the solution within the microchannel and the thin IEM, under an applied electric current, can be locally tuned by the deformation of the microvalve. This tunability provides a robust and simple means of implementing new functionalities into lab-on-a-chip devices, e.g., dynamic control over multiple ICP layers and their associated preconcentrated molecule plugs, multiplex sensing, suppression of biofouling, and plug dispersion, while maintaining the well-known application of microvalves as steric filtration.