Abstract: The surface water, suspended sediment (SS) and surface sediment samples collected in the lower reaches and estuary of Minjiang during 2014 were analyzed. Geochemical characteristics of total carbon (TC) in sediments, their influencing factors as well as the differences among rivers were discussed. The results showed that the average content of TC in the sediments in summer was higher (1.74%), than in autumn (1.70%) at the same stations but with no significant difference. The average content of TC in sediments was 1.82% (1.21%~4.84%) in the study area. The spatial distribution of TC showed a “low-high-low” feature, in other words, the content of TC in sediments increased gradually from Shuikou Reservoir to Fuzhou reach and it reached the highest in Beigang waterway, then decreased gradually towards the estuary and adjacent sea. The high value areas of SS and chemical oxygen demand (COD) were larger in autumn than in summer. The concentrations of SS, COD and particulate TC also showed the distribution that increased first and then decreased, while the content of TC in SS decreased from the reservoir to the estuary. There were significant correlations between TC in sediments and in SS, concentration of SS and COD. Distribution of TC in sediment was influenced by process of deposition-resuspension-redeposition of SS. The major sources of TC were from the inputs of domestic sewage of human activities, organism farming, poultries, animals and aquacultures. The content of TC in sediments of Minjiang Estuary was much lower than those of Yellow River and Yangtze River, while similar to other small and medium-sized estuaries. General speaking, it was at a low level compared with other estuaries, which showed the distribution of TC in sediments was controlled by source rocks, pollutant fluxes and grain size of sediments in different river basins. The content of TC in sediments in Beigang waterway was significantly higher than those in the other rivers, where it indicates that the organic contamination was serious, which will become a potential factor affecting the water quality.