The ability to induce regions of high and low ionic concentrations adjacent to a permselective membrane or a nanochannel subject to an externally applied electric field (a phenomenon termed concentration-polarization) has been used for a broad spectrum of applications ranging from on-chip desalination, bacteria filtration to biomolecule preconcentration. But these applications have been limited by the ability to control the length of the diffusion layer that is commonly indirectly prescribed by the fixed geometric and surface properties of a nanofluidic system. Here, we demonstrate that the depletion layer can be dynamically varied by inducing controlled electrothermal flow driven by the interaction of temperature gradients with the applied electric field. To this end, a series of microscale heaters, which can be individually activated on demand are embedded at the bottom of the microchannel and the relationship between their activation and ionic concentration is characterized. Such spatiooral control of the diffusion layer can be used to enhance on-chip electro-dialysis by producing shorter depletion layers, to dynamically reduce the microchannel resistance relative to that of the nanochannel for nanochannel based (bio)sensing, to generate current rectification reminiscent of a diode like behavior and control the location of the preconcentrated plug of analytes or the interface of brine and desalted streams.