According to Council Directive 98/83/EC on the quality of water intended for human consumption, concentration of the manganese in the drinking water should not exceed 0.05 mg/l. However, this level of manganese concentration is higher in groundwater of a community (Vitia town) in Kosovo. Groundwater is used for drinking supply of some villages and is only chlorified continuing to the reservoir from where is gravitationally disseminated to the villages. The manganese level of the water is at the range 0.3 to 0.6 mg/l. Limestone has been proven by many researchers to be a very effective filter material in manganese removal for groundwater. A miniature filtration unit was modeled to investigate the removal efficiency of manganese. The unit consists of local limestone, where a single material is folded in three layers of different grain sizes. In fact, the aim of this paper was to assess whether limestone as a single material acting as a ”multi-media filter” can reduce the manganese concentration in groundwater. On the basis of the analysis of the single snapshot sample, the removal of manganese achieved more than 95% in filtered water. Particularly, this study demonstrates that filtering the water through three layers of different grain sizes of limestone (“multi-media limestone filter”) can be a good alternative for manganese removal in groundwater.