The plain area in northwestern Shandong province is an important industrial base and grain producing center of China. But this area is lack of groundwater resources and water quality is poor. The content of manganese in local shallow groundwater exceeds the standard seriously. The content of manganese in groundwater is set up by using water samples obtained from the National Groundwater Monitoring Network established in the area. The relationship between manganese content in groundwater and hydrogeological conditions and groundwater environmental chemistry has been analyzed. It is showed that the content of manganese in the shallow groundwater in the study area is relatively high. The average value is 0.847mg/L and the maximum concentration is 4.91mg/L. There are 227 samples exceed Ⅲ grade of manganese content threshold, which covering 81.9%. The lithology of aquifer and groundwater runoff conditions are main factors affecting the migration and enrichment of manganese in shallow aquifer. Some areas with high value manganese are founded controlled by acid environmental condition and seawater intrusion according to human activities. In view of the formation, the excessive manganese in the study area is mainly controlled by high background value.