Unrestricted particle transport through microfluidic channels is of paramount importance to a wide range of applications, including lab-on-a-chip devices. In this article, we study via video microscopy the electro-osmotic aggregation of colloidal particles at the opening of a micrometer-sized silica channel in the presence of a salt gradient. Particle aggregation eventually leads to clogging of the channel, which may be undone by a time-adjusted reversal of the applied electric potential. We numerically model our system via the Stokes-Poisson-Nernst-Planck equations in a geometry that approximates the real sample. This allows us to identify the transport processes induced by the electric field and salt gradient and to provide evidence that a balance thereof leads to aggregation. We further demonstrate experimentally that a net flow of colloids through the channel may be achieved by applying a square-waveform electric potential with an appropriately tuned duty cycle. Our results serve to guide the design of microfluidic and nanofluidic pumps that allow for controlled particle transport and provide new insights for anti-fouling in ultra-filtration.