Pollution discharge disturbs the natural functions of water systems. The environmental microbial community composition and diversity are sensitive key indicators to the impact of water pollutant on the microbial ecology system over time. It is meaningful to develop a way to identify the microbial diversity related to heavy metal effects in evaluating river pollution. Water and sediment samples were collected from eight sections along the Tiaozi River where wastewater and sewage were discharged from Siping City in northeastern China. The main pollutants contents and microbial communities were analyzed. As the primary metal pollutants, zinc (Zn) and arsenic (As) were recorded at the maximum concentrations of 420 and 5.72 ÎŒg/L in the water, and 1704 and 1.92 mg/kg in the sediment, respectively. These pollutants posed a threat to the microbial community diversity as only a few species of bacteria and eukaryotes with strong resistance were detected through denaturing gradient gel electrophoresis (DGGE). Acinetobacter johnsonii, Clostridium cellulovorans, and Trichococcus pasteurii were the dominant bacteria in the severely polluted areas. The massive reproduction of Limnodrilus hoffmeisteri almost depleted the dissolved oxygen (DO) and resulted in the decline of the aerobic bacteria. It was noted that the pollution reduced the microbial diversity but the L. hoffmeisteri mass increased as the dominant community, which led to the overconsuming of DO and anaerobic stinking water bodies. Water quality, concentrations of heavy metals, and the spatial distribution of microbial populations have obvious consistencies, which mean that the heavy metals in the river pose a serious stress on the microorganisms.