Abstract The studied Aptian lacustrine succession of the continental Jatobá Rift Basin varies mainly between pure carbonates (predominantly laminated limestones), marls and shales, with some intercalations of presumably deltaic sandstone complexes. In accordance with geochemical data, the occurrence of dolomite indicates intensive microbial activity in a stratified water column with slightly enhanced salinity. Petrographic data prove mild weathering conditions. Aggregates of authigenic smectite observed in sandstones, probably representing transformed volcanogenic glass particles, strongly indicate explosive volcanic activity. Occasionally occurring dolomite seems to have been formed due to intensive microbial activity under moderately increased salinity conditions. Potential hydrocarbon source rocks containing Type I organic matter (OM) were deposited during various phases of the Aptian. Enhanced biological productivity is indicated by bulk organic geochemical data (C org , hydrogen index, extraction yield) and δ 13 C values of carbonates within peletoidal and laminated limestone layers. Carbon-isotope ratios of carbonates argue for OM cycling and remineralization. High δ 18 O values of carbonates are attributed to periods of lower lake levels. A major contribution of aquatic organisms (green algae, microalgae, zooplankton) and minor input from macrophytes and land plants to OM accumulation is indicated by n -alkane distributions, steroid composition and δ 13 C values of individual biomarkers. Microbial communities included heterotrophic bacteria and cyanobacteria, as well as purple and green sulphur bacteria. The sediments were deposited in an alkaline palaeolake. Highly reducing (saline) bottom water conditions and a stratified water column existed during OM accumulation of the Crato Formation. This is indicated by low pristane/phytane, gammacerane index, and the presence of β-carotane and aryl isoprenoids. Differences in OM composition and stable isotope data reflect the evolution of the basin from a stratified saline lake to a freshwater environment with limited potential for OM preservation.