Abstract: In order to investigate the change of internal structure of porous media caused by arsenic deposition, the X-ray difference micro-tomography was used to characterize the distribution of arsenic aggregates in porous media by scanning arsenic samples prepared in the laboratory and arsenic-rich fluvial sediments from 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 Avizo 6 and Blob3D were used to reconstruct and visualize these 3D datasets. 3D visualization showed that arsenic accumulated in the pore space and grain surface, arsenic aggregates with different sizes had distinctly different morphologies, that is small aggregates tended to be spherical while big aggregates were relatively flat. The research results show that the X-ray difference micro-tomography can be used to observe the pre- and post-deposition structures of porous media and has no any destruction to the samples.