The purpose of the present study is to clarify formation process of the water quality hydrograph. We obtained two ordinary equations to approximately and conveniently express the hydrographs of discharge and water quality. The characteristics of water quality hydrograph observed in mountainous basins can be explained rationally by the method. The method to estimate generation function in formation process of water quality hydrograph using inverse estimation from observed water quality concentration, discharge and rainfall data is newly proposed in this paper. A method is applied to several water quality hydrograph at three different mountainous basins. The result of estimation show eduction and re-suspension is generated from rainfall and influenced by initial condition of water quality concentration.