Sapropels, sedimentary intervals rich in organic matter, represent a substantial carbon source which directly affects the sedimentary redox conditions in marine sediments. While recently-deposited sapropels produce a shoaling of the redox zonation, the long term effect of sapropelic sediments once these become buried over several millennia and lose their most labile carbon fraction requires further addressing. In the northern Black Sea, the changing limnic to marine conditions due to the flooding of the Bosphorous straight and subsequent connection with the Mediterranean Sea circa 9.5 kyr before present (BP), led to local geochemical conditions which favored ocean stratification and an increase in the amount of organic matter reaching the sediment between 8.0 and 3.5 kyr BP. Through reactive transport models which focus on the methane cycle, we track the geochemical effects of the sapropel since its initial deposition up to present time. Our results reveal that, from the onset of their deposition, sapropels heavily influence the methane cycle by controlling the position of the sulfate-methane transition (SMT) through organoclastic sulfate reduction. Nevertheless, the influence of the sapropels on methanogenesis will ultimately depend on the time required for the sapropel to be buried below the SMT. Consequently, methane formation will be favored in locations with high sedimentation rates, or locations receiving turbidites and slumps, such that the sapropel can be quickly buried into the methanogenic zone.