Abstract: Manganese pollution in the Jinjiang watershed of Fujian Province is a key research object. In this study, the entire watershed was divided into 60 sub-watersheds and water quality monitoring sections were set up at the outlets of each sub-watershed. Surface water samples were collected and tested during the flood and dry periods, and the temporal and spatial distribution characteristics of the manganese concentration were analyzed. Combined with flow monitoring and precipitation data, the spatial distribution of manganese load was calculated and analyzed by using hydrological analogy, and the source of manganese pollution was identified based on the load contribution rate. The results showed that the manganese concentration in the flood period was generally higher than that in the dry period, and the manganese concentration in west stream was generally higher than that in east stream. Due to mining, the maximum annual manganese concentration is located at the intersection of the Shuang Stream and the Dashe Stream. In that place the manganese load is much higher in the flood period than that in the dry period, which has a tendency to accumulate downstream with the runoff. The maximum value of manganese occurred at the section of the whole downstream of the Jinjiang watershed. As a result, the identified manganese source areas mainly located in the west stream and sub-watershed near estuary, where should be focused on in the future for comprehensive environmental management work.