This paper is the result of hydrogeological survey engineering. Objective Due to the limitation of terrain conditions, the ecological environment of plateau valley cities is fragile, and the strong human activities have had a severe impact on groundwater. Iron and manganese ions have become the main contribution index of super–class III groundwater in shallow groundwater in Xining, a typical plateau valley city, which seriously threatens the local ecological environment security .and the health of residents. The distribution characteristics and influencing factors of iron and manganese in shallow groundwater in plateau valley cities are deeply explored in order to provide technical support for the prevention and control measures of groundwater pollution and the alleviation of water quality safety problems in this area. Methods Based on the test results of hydrochemical composition of 144 groups of shallow groundwater samples in Xining city, combined with the geology, landform, land use type, hydrogeological investigation data and the influence of human activities, this paper studies the distribution characteristics and influencing factors of Fe and Mn in shallow groundwater in Xining city. Results The over–standard rates of Fe and Mn in shallow groundwater in the study area are 20.98% and 9.79%. Compared with 2012, the contribution rate of Fe and Mn ions to Class Ⅲ groundwater increased by 2 and 3, respectively. The excess rate of Fe and Mn in shallow groundwater of construction land is 1.4 times and 3.47 times higher than that of other land use types, respectively. There are 36 hydrochemical types of shallow groundwater in the study area, and 21 hydrochemical types of groundwater in construction land. Groundwater with high Fe and Mn is mainly enriched in HCO₃–Ca·Mg type water and HCO₃·SO₄–Ca type water. The migration and enrichment of Fe and Mn ions in groundwater are mainly controlled by oxidation–reduction environment, and have no obvious correlation with acid–base conditions, except for the properties of overburden, ground pollution, groundwater runoff conditions. Conclusions The increase of Fe and Mn content in groundwater in the study area is mainly caused by the primary sedimentary environment, while the increase of Fe and Mn content in shallow groundwater in local construction land is caused by the primary sedimentary environment and human activities. Therefore, it is necessary to monitor the Fe and Mn content in groundwater in construction land for a long time and formulate corresponding management measures to prevent the increase of Fe and Mn content in shallow groundwater in the future.