Limited research has been conducted on the heavy metal (loid) (HM) exchanges among seawater, sediments and cultured mussels in mariculture areas. To determine the impacts of mussel mariculture on the transfer and risks of HMs in coastal environments, samples of seawater, sediments and cultured mussels from a typical mariculture area in the South China Sea were analysed. The logarithmic partition coefficients of sediment/water indicated that HMs were preferentially retained by sediments. There were relatively low ecological risks in mussel raft mariculture areas. Principal component analysis and correlation analysis revealed the influences of terrestrial input and ocean circulation on the HMs in seawater, and the bioaccumulation factors reflected the possible accumulation of HMs in seawater by cultured mussels. Mussel farming was the indirect source of HMs in sediments, and the biochemical processes of cultured mussels promoted the transfer and accumulation of HMs into sediments. Health risk assessment revealed that children were more susceptible than adults, and Cd, As and Cr were among the threatening elements. Nonetheless, the health risks that were possibly caused by the daily consumption of farmed mussels were still within safe limits. Thus, the potential pollution remediation and biomonitoring functions of mussel aquaculture in coastal water environments will be further studied in the future.