To study the effects of mining activities on the agricultural environmental quality, four representative paddy fields distributed at different towns (HSG, SNJ, NT and THJ) of Y County, northern Hunan Province, were investigated. It was found that the paddy fields at HSG, SNJ and NT were heavily polluted by heavy metals, especially Cu, Zn and Cd, due to long-term irrigation with the nearby stream water contaminated by mining wastewater. In contrast, the paddy field at THJ, far away from mining sites, was not polluted by heavy metals and regarded as a control. The rice grain produced at the fields of HSG, SNJ and NT had a high risk of Cd contamination. Soil enzyme activities and microbial biomass were significantly inhibited by the heavy metal pollution. Microbial biomass carbon and microbial biomass nitrogen at a severely polluted site of the field at HSG were only 31.6% and 64.4% of the controls, respectively. The activities of dehydrogenase, urease, catalase, acid and neutral phosphatase and sucrase were only 25.2%, 49.3%, 52.4%, 94.7%, 53.2% and 87.8% of the controls, respectively. The microbial parameters were mostly negatively significantly correlated with the contents of Cu, Zn, Cd and Ni in the paddy fields, fully suggesting that the heavy metals had toxic effects on microbial processes. Furthermore, the principal component analysis and cluster analysis indicated that the activities of dehydrogenase and microbial biomass carbon were the most sensitive to the toxicity of heavy metals and could be used as eco-indicators of soil pollution in the study areas. •Paddy fields were polluted by heavy metals due to release of mining wastewater.•Rice grain produced in the polluted fields was contaminated by Cd.•Activities of soil enzymes were highly inhibited by the heavy metal pollution.•DH and MBC could be used as eco-indicators of heavy metal pollution of soils.