Aquaculture in many countries around the world has become the biggest source of seafood for human consumption. While it alleviates the pressure on wild capture fisheries, the long-term impacts of large-scale, intensive aquaculture on natural coastal systems need to be better understood. In particular, aquaculture may alter habitat and exceed the carrying capacity of coastal marine ecosystems. In this paper, we develop a high-resolution numerical model for Sanggou Bay, one of the largest kelp and shellfish aquaculture sites in Northern China, to investigate the effects of aquaculture on nutrient transport and residence time in the bay. Drag from aquaculture is parameterized for surface infrastructure, kelp canopies, and bivalve cages. A model for dissolved inorganic nitrogen (DIN) includes transport, vertical turbulent mixing, sediment and bivalve sources, and a sink due to kelp uptake. Test cases show that, due to drag from the dense aquaculture and thus a reduction of horizontal transport, kelp production is limited because DIN from the Yellow Sea is consumed before reaching the interior of the kelp farms. Aquaculture drag also causes an increase in the nutrient residence time from an average of 5 to 10 days in the middle of Sanggou Bay, and from 25 to 40 days in the shallow inner bay. Low exchange rates and a lack of DIN uptake by kelp make these regions more susceptible to phytoplankton blooms due to high nutrient retention. The risk is further increased when DIN concentrations rise due to river inflows.