An individual-based model based on mussel feeding on algae was developed for the first time, and the model was introduced to a three-dimensional water quality model based on nitrogen, phosphorus, phytoplankton cycling and dissolved oxygen balance, describing the ecological influence of mussel feeding. The drag of aquaculture facilities on suspended farms was introduced to a three-dimensional hydrodynamic model. The water quality model was coupled with the three-dimensional hydrodynamic model to simulate the hydrodynamic environment field of a large offshore suspended mussel farm in Gouqi Island throughout a year. The simulation results agree well with observations. Based on the nutritional restriction approach, the cause of mussel mortality in Gouqi Island is insufficient algal concentration and insufficient filtration rate. Accordingly, an optimized site selection of the suspended mussel farms was proposed, and its feasibility was validated in hydrology and water quality by using the model. Furthermore, hydrodynamic and ecological effects of aquaculture facilities and site selection were quantified. Aquaculture facilities in Gouqi Island reduces surface current speed by 86% and increases half-time of water exchange by 64%. P is the limiting nutrient in the suspended mussel farms of Gouqi Island. The siting of offshore suspended mussel farms only changes the local distribution of nutrients, causing minimal changes in nutrient concentrations and having limited ecological influence.