As a soil filter, the multi-soil-layering (MSL) system has several advantages over some other conventional soil-based systems, including higher hydraulic load rate (HLR) and lower probability of clogging. However, the role of operating factors on the performance of MSL is insufficiently understood, and this limits its further application to some extent. The present paper provides a holistic overview of the crucial operating parameters, including clogging and HLR, aeration, media composition and structure, temperature, and C/N ratio. In particular, clogging and HLR are discussed extensively, since they could cause much greater deterioration over the lifetime of the soil filter than the other factors. There are currently few relevant reports regarding the balance between maintaining the reasonable range of HLR and minimizing less chance of clogging. To fill this research gap, this paper proposes two applicable ways to reduce the opportunity for clogging, namely, system suspension and/or enhanced aeration, which will be time-saving and low cost. In addition, to increase the denitrification capacity of MSL, effluent recirculation is proposed, a novel recommendation based on the municipal wastewater treatment processes, which could also improve the controllability of MSL from the perspective of biochemical reaction.