As the largest container and resource of metals, sediment has a special role in the fate of metals. Factors influencing bioavailability of heavy metals in sediment have never been comprehensively considered and the sediment properties still fail to understand and even controversial. In this review, the mechanisms of sediment properties such as acid-volatile sulfides (AVS), organic matter, texture (clay, silt or sand) and geology, organism behaviors as well as those influencing the bioavailability of metals were analyzed. Under anoxic condition, AVS mainly reduce the solubility and toxicity of metals, while organic matters, Fe-Mn oxides, clay or silt can stabilize heavy metals in elevated oxidative-reductive potential (ORP). Other factors including the variation of pH, redox potential, aging as well as nutrition and the behavior of benthic organism in sediment also largely alter metals mobility and distribution. These factors are often inter-related, and various toxicity assessment methods used to evaluate the bioavailability of trace metals have been also discussed. Additionally, we expect that some novel synthetic materials like polysulfides, nano-materials, provide the substantial amendments for metals pollution in sediment.