Besides nitrate deposits located in the Atacama Desert of Chile and the Mojave Desert of California, the present work documents, for the first time, the occurrence of potassium nitrate as oval-suboval-shaped aggregations associated with the Late Maastrichtian-Early Paleocene Dakhla Shale and the Paleocene-Early Eocene Esna Shale encountered in the northeastern part of the Kharga Oasis, particularly at G. Um El-Ghanayem and G. Ghaneima. Consequently, integrated petrographic, mineralogical, and geochemical investigations were carried out for shale deposits and nitrate salts to reconstruct the paleoenvironmental conditions of shale, reveal the extent to which nitrate salts are genetically related to the paleoenvironment of shale deposits, and build up a complete scenario about the source and the formation mechanism of nitrate salts. The overall results showed that the studied shale deposits were sourced from mafic igneous and quartzose sedimentary provenances where humid climatic conditions were dominant; the transported detrital particles were then settled down under oxidizing bottom water and shallow depositional conditions. Moreover, the nitrate salts are of an epigenetic origin and sourced from the microbial nitrification of organic matter and the wet atmospheric deposition that is believed to be triggered by the active volcanic eruptions during the Late Eocene/Early Oligocene transition where warm climatic conditions prevailed.