In pervious concrete (PC), the permeability decreases as a consequence of the clogging phenomenon that have been widely studied in recent years; however, there is a gap in the knowledge of how this phenomenon affects the internal morphology (micro-scale studies) of the PC, mainly related to pores distribution. Therefore, an experimental program was defined to evaluate the permeability variation caused by the clogging, and the variation of the internal morphology of the PC using 3D microtomography (before and after analysis). For this, three sediments were used to clog the PC (Sand, Clay, and an S + C mixture), adapting the constant head permeability test. All the tests performed globally on the material (porosity, permeability, and clogging) were defined as a macroscale study, and as micro-scale studies the evaluation of internal morphology using 3D microtomography. The macro-scale results showed that the most damaging sediments for PC were the fine sediments (clay and S + C) that achieved permeability reductions of more than 90%. On the other hand, 3D microtomography was shown as a powerful tool in the study of the variation of the morphology of the clogged PC. Through this test, it was possible to identify the variation in porosity depending on the type of sediment, increased frequency of smaller pores (<1 mm) and their influence in permeability variation, their spatial distribution, and finally, the decrease in accessible porosity (connection throats) and this relation with permeability decrease, when fine sediments always being the most damaging.