In this study we investigated the effects of operational parameters of a multi-layered soil filtration (filter depth, filtration velocity, and continuous/intermittent operation) on removal of pollutants in river water. As filter depth increased removal of all the pollutants (COD, TP, TN, and $NH_4$-N) was increased because the increase in filter depth increased in contact time between media and pollutants. The removal of TP and $NH_4$-N more increased with the increase in filter depth, comparing to the biological COD removal which was performed only in the top layer, since the removal mechanism of TP and $NH_4$-N was physicochemical process occurring throughout the whole layers. However, the reduction in filtration velocity resulted in decrease of removal all the pollutants removal due to shorter retention time. Biological COD removal was more influenced with the reduction in filtration velocity (longer retention time), than the removal of TP and $NH_4$-N. Because biological process was occurred only in the top layer which has relatively shorter retention time, comparing with physicochemical process occurred throughout whole media. Therefore, it is desirable that the operation parameters be controlled toward increasing retention time, in order to achieve efficient pollutants removal. The change in operation mode (continuos vs. intermittent operations) did not provide significant effects on the pollutant treatment efficiency by the multi-layered soil filtration system. Our findings suggest that for stable long-term operation it should be considered keeping conditions for biological activity and accelerating clogging.