Provided are an apparatus and a method for river water purification using a treatment soil layer and a permeable filtering medium layer. The river water purification apparatus includes a treatment soil layer and a permeable filtering medium layer which are sequentially and alternately stacked. The treatment soil layer includes a plurality of unit soil layers which are arranged at intervals. A reservoir part which stores a predetermined amount of river water and supplies the river water to an inside of the unit soil layer is provided in an upper end part of the unit soil layer. The permeable filtering medium layer has a higher hydraulic conductivity than that of the treatment soil layer. The river water purification apparatus increases a treatment flux of river water regardless of a coefficient of water permeability of soil and effectively removes nitrogen, phosphorus and nutrient salts by stably forming an anaerobic condition.