The Orava-Nowy Targ Basin (ONTB) is an intramontane depression filled with Neogene and Quaternary deposits located at the junction of the Inner and Outer Carpathians. The Neogene infill of the basin consists mainly of siliciclastic rocks with very common lignite intercalations and is mostly of fluvial or lake origin. The organic matter molecular analysis of seventeen Neogene samples confirmed the terrigenous origin of organic matter with a predominance of higher plant input in most samples, based on the distribution of n-alkanes and steranes, as well as the presence of tri- and tetracyclic diterpenoids, and triterpenoids representing oleanane, ursane, lupane, chrysene and picene derivatives. High concentrations of compounds originating from both angiosperms and gymnosperms suggest the presence of mixed forests. Additionally, important input of mosses into the primary organic matter is indicated by the high concentration of n-C23 and presence of hop-17(21)-enes in most samples. A high Average Aromatic Ring and Conifer Wood Degradation Index > 0.7 indicate high activity of bacteria and wood-degrading fungi in the sedimentary environment. There was no evidence of weathering and scarce signs of biodegradation were identified. All samples were subjected to water washing. Huminite reflectance and biomarker-based parameters, as well as the presence of unsaturated pentacyclic triterpenoids and steroids indicate an immature organic matter. A trend of decreasing maturation of sediments from east to the west was observed, as was a similarity of thermal maturity between the Podhale Synclinorium and the ONTB, although the latter seems to be coincidental. A thermal gradient value of 35 degrees C/km was assumed for calculating the maximum thickness of eroded strata, resulting in 1-1.6 km for the SE area and a maximum temperature of the deepest buried samples equal to 45-65 degrees C.