The toxicities and effects of various metals and metalloids would be misunderstood by health risks based on their concentrations, when their effects on bacterial and ecological functions in soil are disregarded. This study investigated the concentrations and health risks of heavy metals, soil properties, and bacterial 16S rRNA gene in soil around the largest fresh water lake in North China. The health risks posed by Mn and As were higher than those of other heavy metals and metalloids. Mn, As, and C were significantly correlated with the bacterial species richness indices. According to canonical correspondence analysis, species richness was mainly affected by Mn, Pb, As, and organic matter, while species evenness was mainly affected by Mn, pH, N, C, Cd, and Pb. Covariable analysis confirmed that most effects of metals on bacterial diversity were attributed to the combined effects of metals and soil properties rather than single metals. Most bacteria detected in (almost) all soil were identified as Gammaproteobacteria. Specific bacteria belonging to Proteobacteria (Gamma, Alpha, Epsilon, and Beta), Firmicutes, Actinobacteria, Cyanobacterium, Nitrospirae, and Fusobacterium were only identified in soil with high concentrations of Mn, Pb, and As, indicating their remediation potency. Bacterial abilities and mechanisms in pollutant resistance and element cycling in the region were also discussed.