Domoic acid (DA) is a neurotoxin produced by marine microalgae. It tends to accumulate in marine shellfish and fish, posing a threat to aquaculture and seafood consumers’ health. In this study, DA in the surface and bottom seawater, sediment, and porewater of the Jiaozhou Bay, a typical mariculture bay in China, was systematically investigated for the first time over different seasons. Surprisingly, a high concentration of DA was discovered in the marine sediment porewater (maximum detected concentration: 289.49 ng/L) for the first time. DA was found to be extensively distributed in the water body and sedimentary environment of the Jiaozhou Bay. DA in the surface and bottom seawater of Jiaozhou Bay in spring was uniformly distributed, whereas DA showed obvious spatial variations in summer and winter. The high concentration areas of DA are located in the north of Jiaozhou Bay and decreased to the south areas. DA was also distributed in the sediment (spring mean: 316.57 ng/kg; summer mean: 10.22 ng/kg; winter mean: 237.08 ng/kg) and porewater (spring mean: 129.70 ng/L; summer mean: 53.54 ng/L; winter mean: 19.90 ng/L) of Jiaozhou Bay. The DA concentrations in the surface sediment and porewater were higher in the spring than in the winter and summer, contrary to the seasonal variation pattern observed in the surface and bottom seawater. The DA concentration in porewater was significantly higher than in the surface and bottom seawater, indicating that the risk of pollution contamination from DA to benthic fishery organisms may be underestimated. Overall, DA is widely distributed in the seawater and also in the benthic environment of Jiaozhou Bay and exhibited potential harm to fishery organisms varied greatly with seasons. It is an important discovery for marine algae toxins and has important guiding significance and important indicative role for the routine monitoring and management of DA pollution in water and benthic environment.