The migration, transformation, and accumulation of dissolved organic matter (DOM) in pore water of sediment cores play a pivotal role in lacustrine carbon cycling. In order to understand the dynamics of DOM in the sediments of large shallow eutrophic lakes, we examined the vertical profiles of DOM and the benthic fluxes of dissolved organic carbon (DOC) in sediment cores located in algae accumulated, dredged, and central areas of eutrophic Lake Taihu, China. Optical properties showed the significant influence of terrestrial inputs on the DOM components of pore water in the algae accumulated area but an abundant accumulation of autochthonous DOM in the central area. The benthic fluxes of DOC ranging from -458.2 to -139.4 mg·m-2·d-1 in the algae accumulated area displayed an opposite diffusion direction to the other two areas. The flux ranges of 9.5-31.2 mg·m-2·d-1 in the dredged area and 14.6-48.0 mg·m-2·d-1 in the central area were relatively smaller than those in the previously reported lake ecosystems with low trophic levels. Dredging engineering disturbed the pre-dredging distribution patterns of DOM in sediment cores. The deposition, accumulation, and transformation of massive algae scums in eutrophic lakes probably promoted the humification degree of sediments.