A method and a system which enable simple and inexpensive removal of heavy metals from a heavy-metal-containing substance. In this method, a substance containing heavy metals and water are introduced into a mixing bath in proportions by weight of 1:3 to 1:6. A strong acid is added to the mixture, and the mixture is stirred while its pH is maintained at a pH lower than 4. As a result of stirring of the substance at a pH 4, heavy metals are extracted into the liquid as metal ions. The metal-ion-containing liquid is input to a heavy metal precipitation bath, and the pH of the liquid is increased to a pH higher than 10 by addition of alkali to the liquid. Gas bubbles of carbonic acid gas are input to the liquid from a lower portion of the heavy metal precipitation bath, and they are broken into a large quantity of small gas bubbles of carbonic acid gas by turbine blades. The large quantity of gas bubbles of carbonic acid are brought into contact with the metal-ion-containing liquid having a pH higher than 10. As a result, metal ions are precipitated in the heavy metal precipitation bath as carbonates. If the substance is fish or shellfish, alkali and polymer are added to the heavy-metal-removed liquid in the heavy metal precipitation bath, and the liquid is stirred, whereby protein is precipitated.