Abstract: We investigated the spatiotemporal variation of nutrients in the coastal seawater around Weizhou island, Guangxi from 2018 to 2019, and clarified the key factors affecting the nutrient concentration and structure using nutrient budget model from the Land-Ocean Interactions in the Coastal Zone (LOICZ) research program. Furthermore, a flow-through reactor (FTR) experiment was implemented to assess the effects of benthic nutrient fluxes on nutrient concentrations and structures under different organic carbon conditions. The results were as followed: (1) The concentrations of dissolved inorganic nitrogen (DIN) and dissolved inorganic phosphorus (DIP) were affected by nutrient inputs outside the south bay, and their concentrations were higher outside the bay than those inside the bay; (2) The net budget values of DIN and DIP were −9.45×10⁵ mol/a and 0.95×10⁵ mol/a. The DIN input to the bay was mainly attributed to the discharge of groundwater, while the DIN output was mainly due to the uptake of DIN by sediments; the release of phosphorus from the sediments contributed the most of DIP input, and the harvest of shellfish removed 96.6% of DIP; (3) In the FTR experiment, DIN concentration decreased and DIP concentration increased after the seawater flowing through the sediments, and thus the nitrogen phosphorus ratio (N/P) in seawater was reduced. The research can provide a basis for scientific assessment of the potential impact of nutrients on the coral reefs around Weizhou island and reasonable suggestions for the management of coastal environment.