Soil column experiments were evaluated effects of silver nanoparticles (i.e., 0, 2.5, 5, and 10 mg/L) on the microbial viability which is strongly associated with the degradation of organic matter, pharmaceutically active compounds(PhACs) and biological oxidation of nitrogenous compounds during river bank filtration. The addition of silver nanoparticles resulted in almost no change in the aqueous matrix. However, the intact cell concentration decreased with addition of silver nanoparticles from 2.5 to 10 mg/L, which accounted for 76% to 82% reduction compared to that of control (silver nanoparticles free surface water). The decrease in adenosine triphosphate was more pronounced; thus, the number and active cells in aqueous phase were concurrently decreased with added silver nanoparticles. Based on the florescence excitation-emission matrix and liquid chromatograph - organic carbon detection analyses, it shows that the removal of protein-like substances was relatively higher than that of humic-like substances, and polysaccharide was substantially reduced. But the extent of those substances removed during soil passage was decreased with the increasing concentration of silver nanoparticles. The attenuation of ionic PhACs ranged from 55% to 80%, depending on the concentration of silver nanoparticles. The attenuation of neutral PhACs ranged between 72% and 77%, which was relatively lower than that observed for the ionic PhACs. The microbial viability was affected by silver nanoparticles, which also resulted in inhibition of nitrifiers.