—The main factors controlling the bulk sedimentation in the region of the Mendeleev Rise and the adjacent part of the Arctic Ocean during the late Cenozoic were studied using a complex of geomorphological, lithological, and organic geochemical data. Samples for the study were collected during the cruises of the R/V Akademik Fedorov in 2000, 2005, and 2007 and icebreaker Kapitan Dranitsyn in 2012. Analysis of the group and molecular compositions of the dispersed organic matter (DOM) in bottom sediments has shown that the input of terrigenous sediments enriched with abrasion products of lithified rocks from the eastern source province determines the Holocene–Pleistocene sedimentation on the continental slope of the East Siberian Sea and in the Podvodnikov Basin. The individual characteristics of DOM of the late Cenozoic deposits from the underwater mountains of the Mendeleev Rise reflect the wide diversity of sedimentary sources and depositional conditions. Subaqueous erosion and redeposition of denudation products of source rocks and pre-Holocene sediments play an important part in sedimentation together with a terrigenous flow and ice transport.