High resolution synchrotron-based X-ray computed microtomography (X-CMT) was used to identify the morphology of colloidal deposits formed in porous media. We show that difference microtomography - whereby a tomographic reconstruction is performed across an absorption edge - provides valuable information on the nature and location of the aggregates formed by the deposition of colloidal particles. Column experiments were performed using an idealized porous medium consisting of glass beads through which colloidal ZrO2 particles were transported. Tomographic reconstructions of the porous medium and of the aggregate structure provide an unique opportunity to observe colloidal particle deposits and of their morphology. These results show that the local pore geometry controls particle deposition and that deposits tend to form in a rather heterogeneous manner in the porous medium.