Porous media are widely adopted as immobilization sorbents in environmental engineering. The microscale difference in pore structure formation causes significant deflection in a vast landscape. Computational fluid dynamics (CFD) offers a comparative approach to evaluate the individual influence from pore structure formation with strictly controlled surface and volume properties. This paper presents a comprehensive comparison between the performance of cylindrical media and spherical-media in heavy metal immobilization. Digital testing was performed to measure the surface area, specific surface area, density and porosity. Image-based input technique was developed to reconstruct the cylindrical media. It was found that although the surface area, specific surface area and porosity were the same, the spherical media still had an accelerated immobilization rate. Results further showed that the spherical media in floatation arrangement had an immobilization rate of 16% higher than the cylindrical media with the same surface properties. Non-floatation arrangement of the spherical media caused a reduction in immobilization capacity up to 32.8% lower than the cylindrical media. The cylindrical media demonstrated an advantage of being structurally stable under high porosity, the latter of which resulted in an increased immobilization capacity compared with the spherical-media. The results suggest that the cylindrical bio-microstructure is desirable for heavy metal immobilization in a non-flotational environment. The computational approach provides a digital solution to evaluate the immobilization in 3D architected media. The proposed testing methods are feasible for both experimentally obtained images and structures from algorithm-generation.