Metal dynamics and redox states in an ecosystem play crucial roles regulating microbial activity and community structure. We evaluated relationships between soil microbial community and concentrations of six metals under three redox conditions in a river floodplain continuum that was subject to seasonal flooding and metal contamination. Soils were collected from four sites at each of two locations along Tisza River in Hungary. Each soil profile was divided into three redox horizons: aerobic, seasonally reduced, and permanently reduced. Microbial communities were evaluated by microbial biomass carbon (Cmic) and nitrogen (Nmic) contents, dehydrogenase activity, 16S rRNA fingerprints, and culturable bacterial and fungal populations. Of the six metals evaluated, microbial activity and population were closely related to total concentrations of Cu and Cd, followed by Pb and Zn, and least to Cr and Ni in aerobic horizons. Microbial metabolic activity was markedly reduced by increasing metal concentrations with significantly negative correlations between metal concentrations and dehydrogenase activity (r > 0.9*** for Cu and Cd). However, microbial populations were enhanced by increasing metal concentrations with significantly positive correlations between metal concentrations and Cmic, Nmic, cultural bacterial or fungal populations, or soil DNA concentrations (r > 0.9*** for Cu and Cd). Moreover, variations in metal concentrations showed little impact on bacterial diversity and distribution evenness. These results suggest that exposure of microbes to heavy metals at concentrations evaluated suppressed microbial metabolic activity, but did not cause acute toxicity that resulted in cell death and population reduction. In fact, some microbes increased their populations in response to stress conditions. However, microbial community living in reduced horizons demonstrated little responses to variations in metal concentrations, suggesting that either microbial community thriving in reduced conditions was more resilient to environmental stress, or stress factors were markedly suppressed under oxygen limiting conditions.