Epicontinental basins are extremely prone to major paleogeographic changes, and this will directly affect any organic matter (OM) preserved in the depositional record. In this study the Middle–Late Miocene successions in the northern Pannonian Basin System were investigated via sedimentological, petrographic, and geochemical analyses of cores from the Danube Basin to reveal the interplay of factors driving the character of the OM. In the late Middle Miocene (~12.3 Ma), the Central Paratethys Sea maintained normal marine salinity, with dysoxic bottom waters in a distal basin floor environment rich in aquatic OM. The last rifting phase followed during the Late Miocene and led to formation of the deep Lake Pannon. Like seawater, the brackish lake water still also contained sulfate. These open lacustrine deposits (~11.6–10.0 Ma) reveal OM sourced from submerged/floating macrophytes and algae, and humid conditions are indicated by the preponderance of deciduous trees and shrubs on shores. The study identifies hybrid event beds (HEBs) on Lake Pannon's floor (~10.0–9.3 Ma), with currents redepositing mud and OM, resulting in similarities between the Middle Miocene and Late Miocene successions. Turbidite deposition (~9.3–9.0 Ma) from the paleo-Danube induced a shift in OM, replacing algae with terrestrial input. Complete isolation from the main water masses of Lake Pannon (~9.0–8.9 Ma) altered its sources of OM, transitioning from algae to macrophytes, and caused a drop in salinity, likely associated with a humidity peak. The subsequent deltaic dominance (~8.9–8.6 Ma) features well-developed topset lakes, swamps, and floodplain forests, reflecting warm temperate to subtropical climates. The Middle–Upper Miocene deposits studied here are source rocks with fair to very good richness and poor to fair generative potential, and contain kerogen types III and IV, while type II is rare. The rapid paleoenvironmental changes observed over the order of ~100 kyr caused the complete switching of OM type and delivery, giving an indication of the complexity of epicontinental basins.