The effects of the seasonal groundwater level fluctuations on the redox species in groundwater and the microbial communities in aquifer media were investigated at a typical riverbank filtration (RBF) site in northeast China. A total of 50 groundwater samples were collected to illustrate the variations of oxidation-reduction potential (ORP), dissolved oxygen (DO) and redox species such as iron (Fe2+), manganese (Mn2+), ammonium (NH4+), and nitrate (NO3−) during a whole hydrological year. This study observed that the groundwater dynamics fluctuate seasonally with the amplitude of up to 1.0 m, which is mainly related to the hydrological processes of the Songhua river. The groundwater was oxic with an average DO value of 3.6 mg/L and 3.2 mg/L in the two seasons. The ORP measurements showed that the groundwater was mostly under reducing conditions, with the seasonal variations of ORP being concurrent with the water level fluctuation. As electron acceptors, the average values of Fe2+ and Mn2+ were 6.3 mg/L and 6.8 mg/L, and 1.2 mg/L and 1.4 mg/L in wet and dry seasons, respectively. The O2 entrapment induced by the seasonal groundwater level fluctuation facilitates the interaction among O2, Fe2+ and Mn2+ for biotransformation. Moreover, the reductive dissolution of iron and manganese oxides might be major mechanisms for Fe2+ and Mn2+ release under reductive conditions. The average content of NH4+ was 1.5 mg/L and 1.2 mg/L in two seasons, respectively, and NO3− was lower than 0.1 mg/L. The seasonal variation of NH4+ and NO3− in groundwater is mainly related to the periodic application of nitrogen fertilizer in agriculture. The spatiotemporal of microbial communities was significantly different between the two seasons, and Proteobacteria, Actinobacteria, Acidobacteria, Chloroflexi, Firmicutes, Nitrospirae, Gemmatimonadetes, Bacteroidetes, and Verrucomicrobia were the nine main phyla. pH, DO, EC, NO2−, and Fe2+ were the major factors correlating the microbial community in the wet season, while pH, NO2−, NH4+, TH, COD, and SO42− were the critical parameters in the dry season according to RDA results. These results may be valuable to gain insight into the temporal variation of the redox species due to groundwater seasonal fluctuation and to identify the correlation between the groundwater and microbial communities in the redox-dynamic zone.