The coastal plain region usually shows the agricultural dominated industry mode, so more and more attention is paid to non-point pollutants discharge. In this study, the method for assessing the influence of non-point pollutants discharge on river water quality is probed which is concluded as follows: (1) Considering the costal plain island is characterized as nearly even elevation, the conventional gravitational runoff confluence method based on eight-point gravitational flowing directions (D8) is unable to compute the runoff confluence received by the surrounding rivers, so a new method of triangular confluence based on three-points of grid center and the river segments is presented. Further the equations of non-point pollutants loads estimation and non-point pollutants confluence on rivers are presented. (2) The integration mode of non-point pollutants model and river water quality model is presented so as to further assess the non-point pollutants contribution to river water quality. (3) With the Chongming Island, the third largest island in China, as an example, the above-mentioned equations are specified. For this island, the non-point pollutants loads are estimated and linked to the developed water quality model of the river network in the island, and further the non-point pollution evolution in river network is simulated. In this scenario, the non-point pollution contribution to river water quality over the whole island is clearly displayed, and the area where the river water quality is seriously influenced by non-point pollutants discharge is distinctly depicted. This scenario also shows the water quality contribution ratio of non-point pollution to point pollution can be in the range of 55.5% to 44.5% which proves the importance of non-point pollution control in costal plain islands.