Groundwater resources are an essential component of global water resources. Long-term consumption of groundwater exceeding the standard levels for iron and manganese can lead to chronic diseases, posing a threat to human health. The Sanjiang Plain is the largest swamp wetland area in China and has high levels of iron and manganese in the groundwater, but the cause still needs to be clarified. Based on the results of water quality tests of 41 groundwater samples in the Eastern Sanjiang Plain, this paper analyzes the distribution characteristics and causes of iron and manganese from the perspectives of the original strata environment, redox conditions, pH conditions, and hydrochemical indicator factors in the research area, using statistical methods and GIS technology. The results show that high iron and manganese content in groundwater is prevalent in the Eastern Sanjiang Plain, and the exceedance rate of manganese is higher than that of iron (87.80% and 82.90%, respectively). The primary sources of iron and manganese in groundwater are iron and manganese minerals in the original strata environment. Influenced by factors such as acidic conditions, reducing environment, and rich organic matter, insoluble high-valent iron and manganese oxides are reduced to low-valent and soluble divalent iron and manganese. At the same time, groundwater’s high mineralization and evaporation concentration are conducive to increased iron and manganese content, while the influence of human activities is small.