The main characteristics and distribution of organic matter have been studied through several Aptian–Albian lacustrine units (Rio da Batateira, Crato and Ipubı́ Formations, Araripe Basin, NE Brazil). Six main facies have been distinguished on the basis of their lithological–sedimentological characteristics and the type and amount of organic matter: (1) marginal lacustrine deltaic massive to coarsely laminated mudstones and sandstones found as lenticular sheet and channel-infills; (2) oxic marginal lacustrine massive to poorly laminated mudstones; (3) oxic–suboxic inner lacustrine mudstones and laminated bioclastic mudstones; (4) anoxic, inner lacustrine dark mudstones; (5) anoxic, inner lacustrine dark clay-carbonate rhythmites; and (6) anoxic, inner lacustrine finely laminated dark micritic limestones. These facies make up decimeter- to several meter-thick parasequences, which stack up in several tens of meters thick successions. Water level changes and variations of the detritic sediment contribution in the basin controlled the evolution of the depositional system. Palynomorph associations showed that the lacustrine system evolved in an arid–semiarid tropical area where the most characteristic flora consisted of conifers, Gnetales, Bennettitales and early angiosperms. In facies 1 to 3, organic matter was scarce, poorly preserved and mainly derived from higher land plants. Facies 4 is characterised by containing abundant algal/bacterial-derived well-preserved organic matter. Facies 5 and 6 contained mainly branchlets and pollen debris blown by the wind or fed by lacustrine underflows. The pattern of organic matter accumulation and preservation corresponds well with cyclical palaeoenvironmental changes (from anoxic to oxic bottom conditions and from a fresh to saline upper water layer), which affected the shallow lacustrine system. The deposition of thin, organic matter-rich mudstones (facies 4) probably occurred during higher water levels, which resulted in relatively low salinity waters and low detrital contribution to the inner lacustrine zones. Less significant organic matter accumulation is recorded in the clay-carbonate rhythmites and in the limestones (facies 5 and 6) due to scarce autochthonous aquatic organic matter deposition and pervasive intense bacterial degradation, caused by persistent meromictic conditions. Large differences in the degree and path of evolution of the humic material derived from higher land plants have been detected, depending on the depositional conditions. The humic material in the oxic facies underwent humification and gelification and had the highest huminite reflectances, whereas it showed suppressed reflectance values in the oil shales (facies 4) and in the carbonate-dominated facies. In the latter, extensive bacterial reworking of humic material is also observed. These differences are considered significant and applicable to other case studies in terms of evaluating the maturity of organic matter in ancient lacustrine systems.