Within the Russian–German research project on “Siberian River Run-off (SIRRO)” dealing with freshwater discharge and its influence on biological, geochemical, and geological processes in the Kara Sea, sedimentological and organic-geochemical investigations were carried out on two well-dated sediment cores from the Yenisei Estuary area. The main goal of this study was to quantify terrigenous organic carbon accumulation based on biomarker and bulk accumulation rate data, and its relationship to Yenisei river discharge and climate change through Holocene times. The biomarker data in both cores clearly indicate the predominance of terrigenous organic matter, reaching 70–100 and 50–80% of total organic carbon within and directly north of the estuary, respectively. During the last ca. 9 cal ka b.p. represented in the studied sediment section, siliciclastic sediment and (terrigenous) organic carbon input was strongly influenced by postglacial sea-level rise and climate-related changes in river discharge. The mid-Holocene Climatic Optimum is documented by maximum river discharge between 8.2 and 7.3 cal ka b.p. During the last 2,000 years, river discharge probably decreased, and accumulation of both terrigenous and marine organic carbon increased due to enhanced coagulation of fine-grained material.