Iron and manganese are both redox-sensitive elements and important chemical indicators of drinking water quality. The anaerobic hypolimnion caused by thermal stratification results in the release of iron and manganese from sediments in water-supply reservoirs. The exceeding concentration of them may have a great impact on urban water supply. Little research has focused on the relationship between suspended sediment behaviors and the mobilization of iron and manganese in the water-sediment interface of reservoirs. To demonstrate the seasonal variation of iron and manganese and the influence of suspended matter on its behavior in the Biliuhe Reservoir, we comprehensively investigated and analyzed the vertical distribution characteristic of iron and manganese in water, suspended sediments, and sediments from February 2014 to February 2015. According to the results of Spearman correlation analysis, the concentration of iron is highly correlated with total suspended solids, total nitrogen, and total phosphorus, while, the concentration of manganese is significantly correlated with total suspended solids, dissolved oxygen, pH and total nitrogen. Further analysis results indicate that the thermal stratification, the anaerobic hypolimnion, and the resuspension of sediments significantly affect the concentration of iron and manganese in the Biliuhe Reservoir. The average dissolved manganese concentration accumulates on the bottom layer to 0.18 mg/L in the stratified season, while the dissolved iron releases very little from the sediment. The manganese concentration of the surface and middle layers increase to 0.07 mg/L in the mixing season. Because the average concentration of particulate iron in the bottom layer is approximately 0.3 mg/L, the resuspension of sediments may be the main iron source in the bottom layer of the Biliuhe Reservoir. In addition, the flocculated particulate matter and its adsorbed manganese could stay in the reservoir for a long time, so that the content of manganese in the suspended matter is about 7 times higher than that in the surface sediments. Thus, to reduce the impact of elevated iron and manganese concentrations on water supply in the Biliuhe Reservoir, the most effective management practices focused on multi-level intake, hypolimnetic aeration, and amalgamated waterworks, which could ensure the safety of urban water supply in Dalian.