Isotopic, mineralogical, and elemental analyses have been conducted for the geochemical characteristics of the bulk carbonates in the sediment cores from the Western High and Çınarcık Basin in the Sea of Marmara to investigate the authigenic, biogenic, and detrital components and their possible use in paleoceanographic studies. The Western High is a relatively shallow (−500 to −800 m) compressional area characterized by relatively low sedimentation rates (30–40 cm/Kyr), whereas the Çnarcık Basin is a deep (~1,250 m) transtentional area represented by high sedimentation rates (>1 m/Kyr). Both 87Sr/86Sr and δ18O of bulk carbonates from the Western High exhibit significant variations, increasing steeply from 87Sr/86Sr of 0.708437 to 0.708916 and δ18O of −3.2‰ Vienna Pee Dee Belemnite (VPDB) to 0.1‰ VPDB, indicating the incursion of the Mediterranean seawater after the last glacial and reflected in the change from lacustrine to marine environment. However, bulk carbonates in the core from the Çınarcık Basin have comparatively uniform values of 87Sr/86Sr (~0.708845) and δ18O (~0.0‰ VPDB), implying that this core did not experience the lacustrine/marine transition. In the Western High, δ13C values up to +24.3‰ VPDB at 400 cm below seafloor reveal the mineralization of heavy CO2, providing independent evidence for the subsurface biodegradation of petroleum. While in the Çınarcık Basin, δ13C values of bulk carbonates were relatively constant (approximately −2.94‰ VPDB). The high δ13C values of bulk carbonates from the Western High reflect the dissolution of primary carbonates as a result of the local acidic environment and precipitation of authigenic carbonates later, supported by mineralogical and elemental results.