<p>The exchange of inorganic nutrients at the coastal sediment-water interface (SWI) plays a crucial role in regulating the nutrient budget in overlying water. The related studies mainly focus on the mid-to high-latitude regions, leaving a significant gap in the quantitative assessment of nutrient exchange and environmental controls at the SWI in low-latitude coastal regions. We quantitatively assess the exchange of inorganic nutrients at the SWI in three tropical bays (Dongzhai Harbor, Xiaohai Lagoon, Qinglan Harbor). Sediments act as a source of ammonium, phosphate, and silicate, but for nitrate, sediments can be both a source and sink, although with substantial spatial and temporal variations in their fluxes. Labile organic matter is a critical regulator for the fluxes of inorganic nutrients at the SWI. The sedimentary nutrients input with high N/P molar ratio will alter the nutrient stoichiometry to mitigate the nitrogen limitation in coastal waters. However, the internal sediment release in these tropical bays plays a relative weak role in contributing to the nutrient addition in comparison with the other external nutrient sources including riverine input, submarine groundwater discharge, and atmospheric deposition. According to the global compilation on SWI nutrient fluxes, we propose that water column primary production and external inputs to interpret the variation in exchange and fluxes of nutrients at the SWI in different ecosystems. Such a conceptual understanding of these chain biogeochemical processes involving external nutrient input, primary production, particulate organic matter settling, and the accumulation and release of inorganic nutrients in sediments will be helpful for the scientific-based pollution prevent and control in coastal waters.</p>