The structural organization inside the concentration polarization layer during cross-flow membrane separation process of Laponite colloidal dispersions has been characterized for the first time by in situ time-resolved small-angle X-ray scattering (SAXS). Thanks to the development of new "SAXS cross-flow filtration cells", concentration profiles have been measured as a function of the distance z from the membrane surface with 50 mu m accuracy and linked to the permeation flux, cross-flow, and transmembrane pressure registered simultaneously. Different theological behaviors (thixotropic gel with a yield stress or shear thinning sol) have been explored by controlling the mutual interactions between the particles as a result on the addition of peptizer. The structural reversibility of the concentration polarization layer has been demonstrated being in agreement with permeation flux measurements. These observations were related to structure of the dispersions under flow and their osmotic pressure.