In the paper we present the evaluation of the effectiveness of the removal of biogenic compounds and indicator bacteria from domestic sewage in a vertical flow filter with a variety of fillings. The research was carried out on expanded clay, zeolite, calcined siliceous limestone, and crushed PET flakes. Based on the study of raw and treated wastewater, the effectiveness of removal of ammonium nitrogen, orthophosphates, Escherichia coli, and coliform bacteria was determined according to the selectivity, porosity and grain size of the fill. In the case of removing biogenic compounds, the most effective fillers were found to be of natural porous selective materials, such as zeolite and calcined siliceous limestone. They produced a very high removal rate of ammonium and orthophosphate, amounting to 75.34%, and over 79%, respectively. It has been demonstrated that the filter that was filled with natural porous material of fine particle size (the zeolite) was the most suitable for the removal of indicator bacteria. A very high degree of the Escherichia coli (99.98%) and coliform bacteria (99.94%) reduction was obtained.