Variations in environmental and biological origins contributing to the heterogeneity of lacustrine source rocks can be illustrated in their diverse genetic facies. The Zhu 1 depression, eastern Pearl River Mouth Basin, South China Sea, is characterized by two thick, Paleogene, organic-rich synrift units, the Wenchang and Enping Formations. The integration of bulk geochemical and biomarker data with tectonic and sedimentary information provides the basis for a comprehensive assessment of the environmental and ecological changes through geologic time and their impact on the heterogeneity of these lacustrine source rocks. Both the Wenchang and Enping Formations display wide variations in total organic carbon content and hydrogen index values as well as biomarker composition, suggesting lateral and chronological changes in organic facies. Using gas chromatography–mass spectrometry and hierarchical cluster analysis, five genetic facies were identified within these two source horizons. These facies represent different organic-matter inputs and sedimentary and early diagenetic environments based on their distinctly different assemblages of 11 source-dependent biomarker ratios. Four facies were distinguished in the Wenchang Formation, and two facies were distinguished in the Enping Formation, with one being common to both formations. During the middle Eocene, the Wenchang Formation was deposited in a series of small, deep lakes of laterally variable salinity, acidity, and biofacies. During the deposition of the Enping Formation in the late Eocene and early Oligocene, the previous lakes merged into fewer lakes with shallower depth and larger areal coverage, with the biota becoming more uniform across the whole depression. The coevolution of these lacustrine settings and their biota is closely associated with the development of the Zhu 1 depression, within which multiple separate sags produced by rapid mid-Eocene subsidence finally merged into a single depositional unit during slow subsidence in the late Eocene and early Oligocene. Accordingly, an integrated model was established to provide an overview of the contrasting origins of lacustrine source rocks during the two Paleogene epochs. This model may have important implications for source-rock prediction in the undrilled parts of the basins or for reference to source-rock heterogeneity in other rift basins.