The sea area of Changhai County in Dalian City is a typical floating raft aquaculture area, located in Liaoning Province, China, where a key issue in determining the scale and spatial layout of the floating raft aquaculture is the assessment of the impact of aquaculture activities on the hydrodynamic environment. To address this issue, we established depth-averaged two-dimensional shallow water equations and three-dimensional incompressible Reynolds-averaged Navier–Stokes equations for the open sea area described in this paper. The impact of floating rafts for aquaculture on hydrodynamic force was reflected in the numerical model by changing the Manning number, where scenarios with different aquaculture densities were taken into account. Finally, the water exchange rate of the floating raft aquaculture area in the study area was calculated. It was found, through a comparison between the simulated value and the measured value obtained via layered observation, that the two values were in good agreement with each other, indicating that the model exhibits great accuracy. In addition, the calculation results for scenarios before and after aquaculture were compared and analyzed, showing that from low-density to high-density aquaculture zones, the variation in flow rate was greater than 80% at the peak of a flood tide. The water exchange rates of the water body after 1 day, 4 days, and 8 days of water exchange were also calculated, and the results show that they had been reduced by 17.92%, 13.59%, and 1.63%, respectively, indicating that the existence of floating rafts for aquaculture indeed reduced the water exchange capacity of the water body. The model described in this paper can serve as a foundation for other studies on aquaculture in open sea areas, and it provides a theoretical basis for the scientific formulation of marine aquaculture plans and the rational optimization of the spatial layout.