This paper analyzed the spatiotemporal distribution of heavy metals in 6746 samples of aquatic organisms (fishes, shrimp and crabs), to make health risk assessments of six heavy metals (As, Cd, Cr, Cu, Hg and Pb). The results indicated that there were significant differences of heavy metal concentrations between different groups of aquatic organisms, months and provinces. The concentrations of Cd, Cr, Hg and Pb varied greatly within one year, with levels higher in summer and autumn, and lower in spring and winter. Crabs in Shandong, Shanxi, Zhejiang and Shanghai posed a high risk of Cd exposure, with the average Cd level exceeding the limit set by China (0.5 mg/kg, w.w.). In addition, the average TR value in sea crab was greater than 10, indicating a high cancer risk. However, the average THQ values of the six metals were all below 1 in China, and there was no overall non-carcinogenic risk.