The inflow of heavy polluted tributaries is one of the main factors that destroy the water quality at the river confluence area and downstream, especially in the wide-shallow river confluence area. In this study, a generalized model of a two-dimensional confluence was established and validated, and dissolved oxygen concentration was used as the water quality indicator. The influence laws and mechanisms of different spur dike layout patterns on the water quality distribution characteristics and the transport and mixing processes at the confluence were explored through numerical simulation. The results show that there is a large area of water pollution at the confluence with the polluted tributary, which is distributed near the outlet of the tributary, and the water quality in this area recovers slowly. The flow ratio is the main factor affecting the distribution of water quality transport at the confluence. Arranging dikes on the opposite bank of the tributary can significantly reduce the area of pollution by adjusting the flow field. Arranging dikes on the tributary side of the confluence can effectively promote water quality mixing through vortex suction between dikes and improve water quality near the tributary side of the river bank. The dissolved oxygen concentration between dikes at the river bank on the tributary side showed an increasing trend along the river direction, and vortex flow velocity showed a decreasing trend, and the increment of dissolved oxygen concentration had a good linear correlation with the interval between dikes and the change in vortex flow velocity between dikes.