An increasing number of marine aquaculture facilities are being placed in shallow bays and open sea. In this study, we present a coupled hydrodynamic and solute transport model with high-resolution schemes in marine aquaculture waters based on depth-averaged shallow water equations. A new expression of drag force is incorporated into momentum equations to express the resistance of suspended culture cages. The coupled model is used to simulate the effect of suspended structures on the tidal current and the motion of a contaminant cloud in the marine aquaculture of the North Yellow Sea, China. Simulation results show a low-velocity area inside the aquaculture cage area, with a maximum reduction rate of velocity close to 45% under high-density culture. The results also show that the tidal currents are sensitive to the suspended cage densities, cage length and drag coefficients of cages. The transport processes of pollutants inside aquaculture facilities are inhibited away from the vicinity of the culture cage area because of the reduction in tidal currents; therefore, the suspended cages significantly affect the transport processes of pollutants in coastal aquaculture waters. Furthermore, the reduction in the horizontal velocity can significantly decrease the food supply for aquaculture areas from the outside sea. The results of this study provide new insight into the planning of high-density suspended facilities for coastal aquaculture activities.