Submerged fault ruptures generate earthquake-triggered mass flow deposits, which are extensively used as a tool in subaqueous paleoseismology. In tectonically active deep sedimentary basins, such as the Sea of Marmara (SoM), these mass flow deposits are defined as turbidite-homogenite units (THUs), consisting essentially of a coarse basal part and an overlying homogeneous mud (homogenite). Detailed characterization of THUs is crucial in order to establish meaningful criteria to link these units with earthquakes events and to identify their transport routes and depositional mechanisms. Here, we combine μ-X-ray Fluorescence (μ-XRF), Anisotropy of Magnetic Susceptibility (AMS) and additional rock magnetism analyses of a 21-m long piston core from the Kumburgaz Basin of SoM to define the upper stratigraphic boundary of THUs with hemipelagic sediments and investigate the controls of hydrological changes on turbidite frequency and thickness over the last 15 kyrs BP. The sedimentary succession of this period includes a lower lacustrine and an upper marine unit with two Holocene sapropel intervals. The sequence is interrupted by a total of 70 THUs, characterized by a significant magnetic foliation related to the depositional setting rather than the magnetic signature. Magnetic mineralogy of the coarse basal parts of THUs have more ferromagnetic particles than the overlying homogenites and background sediments. While the homogenite parts have a more constant mineralogy than the basal parts, they do not differ the background sediments. Based on an event-free chronostratigraphic model derived from radiocarbon ages and the published age of lacustrine-marine (L-M) transition, the average THU occurrence intervals in the lacustrine (14.8–12.6 kyrs BP), lower sapropel (11.2–5.7 kyrs BP), upper sapropel (5.4–2.7 kyrs BP) and non-sapropelic part of the marine unit (2.7 kyrs BP-present) are 235 yrs., 287 yrs., 114 yrs. and 160 yrs. respectively. The average thickness of the THUs in the same units are 20.8 cm, 15.7 cm, 6.1 cm and 6.1 cm. The variability of average THU occurrence intervals and THU thicknesses are controlled by the sea level rise and salinity increase following the full marine connection of the SoM at 12.6 kyrs BP, which caused changes in slope stability, sediment composition and sediment deposition in different parts of the basin. Geomechanical properties of the lower sapropel appears to have been important in resulting long THU recurrence intervals and relatively high THU thicknesses.