Microbial biofilms are observed in both natural and engineered subsurface environments and can dramatically alter the physical properties of porous media. Current understanding of biofilm formation and the associated impacts to structural and hydrodynamic properties of porous media are limited by our ability to observe changes to pore morphology non-destructively. Imaging biofilm within opaque porous media has historically presented a significant challenge. X-ray computed microtomography has traditionally been used for non-destructive imaging of a variety of processes and phenomena in porous media, however, the conventional contrast agents used in tomography research diffuse quite readily into both the aqueous phase as well as the porous media-associated biofilm, thereby preventing delineation of the two phases. Two new methods for imaging biofilm within porous media using x-ray microtomography will be presented. The first method utilizes silver-coated glass microspheres as a surface attached contrast agent for delineating the biofilm-aqueous phase interface within porous media. The second method introduces a barium sulfate suspension to the aqueous phase which is excluded from the biofilm matrix, thereby allowing direct segmentation of the solid, biofilm, and aqueous phases. Imaging results using both of these methods will be presented along with the respective advantages and limitations. Quantitative analysis of biofilm formation and changes to macropore morphology will also be presented, along with potential applications for these methods.