Abstract: The lagoon serves as a natural breeding ground with ecological functions such as coastal protection and storm shelter. However, pollutants generated by human activities in the region may pose health threats to the environment. Therefore, conducting a study on the presence of pollutants is a crucial measure to maintain ecological balance in the lagoon and protect its fishery resources. The occurrence of polycyclic aromatic hydrocarbons (PAHs), organochlorine pesticides (OCPs), and polychlorinated biphenyls (PCBs) was analyzed by using high throughput analytical technique. The results show that the concentrations of ΣPAHs, ΣOCPs, and ΣPCBs are in the range of 12.19-291.07 ng/L, 17.40-80.79 ng/L and 0.49-2.74 ng/L in Lingshui Lagoon. Both ΣPAHs and ΣOCPs are significantly influenced by human activities, with higher concentrations observed in the coastal areas compared to the lagoon interior. In the surface water, PAHs are primarily dominated by low molecular weight compounds (94%). OCPs are predominantly composed of hexachlorocyclohexanes (HCHs) (42%), primarily derived from the input of lindane. PCBs are primarily composed of dichlorobiphenyls (37%), possibly originating from atmospheric deposition and unintentional human activities. The results of risk entropy analysis indicate that the surveyed area possesses a certain level of ecological risk, with PCB206 being the primary ecological risk component.