<p>Rapid increased nuclear power plants along the cost in China, as well as intensive nuclear activities over the world has raised a big concern on the marine environmental safety. The distribution patterns and transport pathways of artificial radionuclides in the marginal seas of China is important for mitigating impact of radioactive pollution discharged to the seas. ¹²⁹I is an excellent tracer for investigating the transport and diffusion of water-soluble radioactive pollutants in the marginal seas because of its long half-life, high solubility in seawater and conservative feature in the ocean. In this work, seawater samples were collected from surface and different depth in the stations in the northern South China Sea (NSCS) and analyzed for ¹²⁹I and ¹²⁷I using a sensitive analytical method established in our laboratory. The level and distribution of ¹²⁹I in this region were obtained, and the sources, transport and migration of ¹²⁹I in the NSCS were investigated. It was revealed that terrestrial input via rivers is the primary source of significantly higher ¹²⁹I levels in the Pearl River estuary (with ¹²⁹I/¹²⁷I atomic ratios from 6.0×10⁻¹¹ to 38×10⁻¹¹, compared to (4.0–6.6)×10⁻¹¹ in surface seawater in the open sea in this region). While, the level of stable iodine isotope (¹²⁷I) was significantly lower in the estuary area compared to the open sea. The atomic ratios of ¹²⁹I/¹²⁷I peaked in the subsurface layer in the open sea in the NSCS. By estimating the distribution of ¹²⁹I inventory in this sea area, the contributions of different input modes in this region were assessed to be in a order of the ocean current input&gt;river input&gt;direct atmospheric fallout. These results are useful for predicting the diffusion pathways and impacts of nuclear pollution in the event of accidents in marginal seas and for assessing environmental radiation safety.</p>