Abstract:[Background] Research on the causes of the pollution in reservoir water often focuses on water eutrophication, and the changes of pH value, dissolved oxygen, ammonia nitrogen, and total bacterial count. However, a few studies on the seasonal variation pattern of heavy metal content and environmental factors and the correlation between the heavy metal content and different environmental factors are available. In addition, there is no report on the diversity of in-situ microbial populations in typical seasons. [Objective] To detect the seasonal variation of the concentration of Mn2+ and Fe2+ and different environmental factors in the bottom water of Changtan reservoir, Taizhou city, Zhejiang province, analyze their correlation, enrich functional microbial consortia at the bottom of the reservoir in normal (February) and wet (August) periods, and elucidate the difference in the species and diversity of the enriched microbial communities. [Methods] The bottom water of the reservoir was filtrated and the functional microbial consortia was enriched. The V3–V4 regions of 16S rRNA genes were sequenced and the community structure was analyzed. All tests were carried out according to the Standard Examination Methods for Drinking Water (GB5750-2006). [Results] The concentration of Mn2+ and Fe2+ in the water of Changtan reservoir changed seasonally. The concentration of Mn2+ and Fe2+ (initial 0 mg/L) in the water began to slowly increase in the spring-summer succession period every year, peaked in summer and autumn, and then decreased to below the detection limit in the late autumn and early winter. Among the detected environmental factors, the concentration of dissolved oxygen in water, ambient temperature of reservoir, and precipitation showed obvious seasonal changes. The concentration of Mn2+ and Fe2+ had a positive correlation with temperature, precipitation, and turbidity but a negative correlation with dissolved oxygen concentration, pH value, and total phosphorus concentration. In the correlation analysis, the concentration of two metal ions had the strongest correlation with dissolved oxygen concentration, followed by ambient temperature and precipitation. The species and diversity of functional microbes were significantly different between the normal and wet periods. Only Acinetobacter and Sediminibacterium were detected in the wet period, accounting for about 50% each, while the normal period was dominated by 9 genera, such as Bacillariophyta (47.62%) and Limnohabitans (9.52%). The culturable consortia from water in the normal period and wet period both can remove the Mn2+ in the reservoir water, and the removal rates were about 35.9% and 11.4%, separately. [Conclusion] The concentration of Mn2+ and Fe2+ in the bottom of Changtan reservoir changes seasonally with different environmental factors, and the concentration of Mn2+ and Fe2+ shows different correlation with different environmental factors. The structures of the two functional microbial communities enriched in wet and normal periods are different. This study provides microbial resources for the treatment of heavy metal-polluted water by microorganisms, and has a certain reference value for realizing the goal of “beautiful countryside” in China.