Although sub-salt portions of the Atafona Formation—lacustrine deposits from the rift phase of the Campos Basin, Brazil—have been drilled in recent decades, no recent studies have focused on this new data from the formation. Additionally, detailed studies on the clay mineralogy of the formations are lacking, and there is also a gap in our understanding of the depositional evolution of the Atafona Formation. In this study, we used cutting samples from a pre-salt well to provide novel data and interpretations on the lithogeochemistry, mineralogy, depositional environment, and sediment provenance of the formation’s entire drilled interval. Analyses included X-ray fluorescence (XRF), inductively coupled plasma mass spectrometry (ICP-MS), X-ray diffraction (XRD)—including clay mineralogy—and scanning electron microscopy with energy-dispersive spectroscopy (SEM-EDS), in addition to well log correlation. The primary clay mineral identified is saponite, with geochemical and fabric characteristics indicative of authigenesis, suggesting an alkaline paleoenvironment. Cycles of wetter periods, marked by increased detrital input, and drier periods, marked by increased carbonate formation, were identified. An increase in phosphorus, sulfur, dolomite, and strontium in the upper Atafona Formation suggests a possible growth in microbial activity. Elemental ratios indicate that the origin of acidic-to-intermediate igneous rocks causes the formation of detrital grains, although we propose an additional mafic source of calcium and magnesium supplied by groundwater flowing through the basaltic basement.