The effect of hydraulic loading rate (HLR) and media type on the removal of bulk organic matter and nitrogen from primary effluent during soil aquifer treatment was investigated by conducting laboratory-scale soil column studies. Two soil columns packed with silica sand were operated at HLRs of 0.625 and 1.25 m/d, while a third column was packed with dune filtering material and operated at HLR of 1.25 m/d. Bulk organic matter was effectively removed by 47.5 ± 1.2% and 45.1 ± 1.2% in silica sand columns operated at 0.625 and 1.25 m/d, respectively and 57.3 ± 7.6% in dune filtering material column operated at 1.25 m/d. Ammonium-nitrogen reduction of 74.5 ± 18.0% was achieved at 0.625 m/d compared to 39.1 ± 4.3% at 1.25 m/d in silica sand columns, whereas 49.2 ± 5.2% ammonium-nitrogen reduction was attained at 1.25 m/d in the dune filtering material column. Ammonium-nitrogen reduction in the first 3 m was assumed to be dominated by nitrification process evidenced by corresponding increase in nitrate. Part of the ammonium-nitrogen was adsorbed onto the media, which was observed at higher rates between 3 and 5 m in silica sand column operated at HLR of 0.625 m/d and dune filtering material column operated at 1.25 m/d compared to 1.25 m/d silica.