Stratigraphic forward modelling was used to simulate the deposition of Upper Cretaceous, Eocene and Oligo‐Miocene source rocks in the Eastern Mediterranean Sea and, thus, obtain a process‐based 3D prediction of the quantity and quality distribution of organic matter (OM) in the respective intervals. Upper Cretaceous and Eocene models support the idea of an upwelling‐related source rock formation along the Levant Margin and the Eratosthenes Seamount (ESM). Along the margin, source rock facies form a narrow band of 50 km parallel to the palaeo shelf break, with high total organic carbon (TOC) contents of about 1% to 11%, and HI values of 300–500 mg HC/g TOC. On top of the ESM, TOC contents are mainly between 0.5% and 3% and HI values between 150 and 250 mg HC/g TOC. At both locations, TOC and HI values decrease rapidly towards the deeper parts of the basin. In the Oligo‐Miocene intervals, terrestrial OM makes up the highest contribution to the TOC content, as marine organic matter (OM) is diluted by high‐sedimentation rates. In general, TOC contents are low (<1%), but are distributed relatively homogenously throughout the whole basin, creating poor quality, but very thick source rock intervals of 1–2 km of cumulative thickness. The incorporation of these source rock models into a classic petroleum system model could identify several zones of thermal maturation in the respective source rock intervals. Upper Cretaceous source rocks started petroleum generation in the late Palaeocene/early Eocene with peak generation between 20 and 15 Ma ca. 50 km offshore northern Lebanon. Southeast of the ESM, generation started in the early Eocene with peak generation between 18 and 15 Ma. Eocene source rocks started HC generation ca. 25 Ma ago between 50 and 100 km southeast of the ESM and reached the oil to wet gas window at present day. However, until today they have converted less than 20% of their initial kerogen. Although the Miocene source rocks are mostly immature, Oligocene source rocks lie within the oil window in the southern Levant Basin and reached the onset of the wet gas window in the northern Levant Basin. However, only 10%–20% of their initial kerogen have been transformed to date.