In order to investigate the change of internal structure of porous media caused by arsenic deposition, X-ray difference micro-tomography was used to characterize the distribution of arsenic aggregates within porous media by scanning a series of arsenic samples prepared in the laboratory and arsenic-rich fluvial sediments from the Río Loa in Chile. After image processing, background noise in the tomograms was reduced and arsenic information was enhanced. Then the processed images were used to generate 3D spatial distribution datasets of arsenic in the media. Tools like Avizo6 and Blob3D were used to reconstruct and visualize the 3D datasets. 3D visualization showed that arsenic accumulated in the pore space and grain surface; arsenic aggregates of different sizes had distinctly different morphologies, which small aggregates tended to be spherical while big aggregates were relatively flat. These results show that difference micro-tomography can be used to observe the pre- and post-deposition structure of porous media, without any destruction to the samples.