This study was conducted to determine the content of mercury in the flowing river around small-scale gold mines. Mining wastes from the run of mining are dumped into the watersheds and potentially contaminate the water and sediment in the watershed near the gold mining area. We analyzed the characteristics of the waste and the result was compared with the water quality standards (Environment Minister Decision No.202 of 2004 and Government Regulation No.82 of 2001) and sediment quality standard (the Canadian sediment quality guidelines for the threshold effect level (TEL) and probable effect level (PEL)). We found that wastewater from the gold mining areas was categorized in class IV. The mercury content in the sediment samples did not meet the standards of Canadian sediment quality guidelines for TEL. The content of mercury in the sediment samples from the gold mine site was very high. The sediment mercury samples had been settled for a long time around the watershed. The content of mercury in the mining location indicated that mercury had been contaminating the area around the small-scale gold mining.