This research investigated to reduce mass of heavy metals in AMD(acid mine drainage) by microbial mats formed on the channel bed. As, Cd, Cu, Fe, Mn and Zn components were monitored in water and microbial mats, at three points (AMD1, AMD2 and AMD3), in a total of six times. Average daily discharge mass of heavy metals was highest in July, Fe component contained more than 76% of total discharge mass. Discharge mass of heavy metals of AMD and heavy metal contents in microbial mats decreased with downstream at channel. Heavy metal components that average daily discharge mass is over 0.5 kg were Fe, Cu and Zn, and they were highest in July. Average removal efficiency of heavy metals in AMD was highest about 21% in Fe, this microbial mats were due to form from precipitation of Fe component in AMD by aerobic iron bacteria. Relative content for As component in microbial mats than AMD was over 16 times, this As components were due to absorb at iron oxide and iron hydroxide on the surface of microbial mats.