In order to timely and quantively research the effect of groundwater recharge on river concentration diffusion,taking a plain river as study object,the paper cut apart the total flow of river by base flow separation method based on the suppose of line source supply.It built a traditional model which didn't consider the effect of groundwater recharge and a new model after the total flow was separated by the aid of AD module of MIKE 11. Through the analysis of the process of concentration diffusion in some points of the river on time,it researched the difference between two models and its cause in quantity. The results demonstrated that the difference of steady value of upstream concentration curve in two models is 3%,the growth process has higher anastomosis. The downstream concentration decays quickly in new model. The difference of concentration between two models is huge and reaches 1000 times. It has a huge impact on the result of river quality diffusion whether the river flow is studied in splitting.The impact can quickly become large with the increase of distance of groundwater recharge.