Aquatic macrophytes form a “system” consisting of the macrophytes themselves and periphytons attached to them. The system has a significant role in purifying water. In this study, we evaluated such water purification functions of macrophytes-periphytons “system”, as removing nutrients of the river water prior the river flowing into a lake. Using the data obtained by a field survey and laboratory tests, we made a model of the water quality purification by macrophytes and the periphytons. As a result, we found (1) the “system” of aquatic macrophytes and periphytons play a role as “catalysis” to suspend the dissolved nutrients, and (2) a physical purification function by the aquatic macrophytes which act as a filter to remove suspended solid from the water. Also, we clarified the efficiency of these functions at the water surface.