The Lower Permian Irati Formation in the northeastern and central eastern Paraná Basin (southern Brazil) was investigated in terms of bulk and molecular organic geochemistry in order to enlighten the complex depositional paleoenvironment during deposition of Irati black shales. The geochemical data reflect temporal and spatial variations of freshwater incursions promoting salinity stratification and high primary productivity in surface waters with the establishment of photic zone euxinia. Overall, highly concentrated C 17 long-chain alkylnaphthalenes point to algal blooms as a result of freshwater inflows into the Irati Sea, mostly in the central eastern basin segment, and resemble concentration variations of pristane, phytane and nC 17 . The freshwater inflows were also retraced by increasing chroman ratios toward the top of the investigated units along with the general decrease of further palaeosalinity indicators, e.g., gammacerane, tetracyclic (C 24 ), β-carotane, and the herein suggested γ-carotane and lexane indexes. The existence of a water column stratification promoting organic matter preservation is supported by the detection of tetrahydrophenanthrene at high concentrations, in addition to the known prominent occurrence of gammacerane. The detection of C 10 to C 31 aryl isoprenoids in addition to C 16 and C 18 pseudohomologue aryl isoprenoids points to the presence of photic zone euxinia. In general, samples from the central eastern basin were deposited in a deeper marine setting with lower salinity than samples from the northeastern basin, which displays signals of a shallower marine environment with reducing bottom water conditions, both deposited under freshwater influxes.