The study investigates the impact of pore structure parameters of three chemically non-active filtration materials on the auto-activation time and the height of the filtration zone for manganese removal from groundwater. At a technical scale, the activation is a long process which may require a period of up to three months. The process can be shortened by the use of porous filtration materials. In this study, three filtration materials (silica sand, chalcedonite sand, GAC—granulated activated carbon) were investigated using subcritical nitrogen adsorption and mercury injection capillary pressure measurements. These methods provide a comprehensive evaluation of pore structure parameters, including specific surface area (SSA), micro- and mesopore volumes, and an extended range of pore size distribution (PSD). The studied materials provided a wide range of micro- and mesopore volumes as well as SSA. In order to investigate the auto-activation time of filtration material—the time required to achieve the requested quality of the filtrate—and the height of the filtration zone, a pilot experiment was conducted for 1950 h. The pilot installation consisted of three-meters-high (10 cm diameter) filtration columns filled with the tested filtration materials. The results indicate that the internal pore structure and the investigated auto-activation parameters are correlated. Both auto-activation time and the size of the filtration zone were influenced by the mesopore volume and the associated SSA of the tested materials. The micropore volume was less effective in improving the autoactivation parameters. The research results indicated the importance of pore structure characteristics which should be considered prior to time-consuming pilot and technological tests.