This study investigates the process of formation of ooidal ironstones in the Upper Cretaceous-Paleogene succession in western Siberia. The formation of such carbonate-based ironstones is a continuing problem in sedimentary geology, and in this study, we use a variety of data and proxies assembled from core samples to develop a model to explain how the ooidal ironstones formed. Research on pyrite framboids and geochemical redox proxies reveals three intervals of oceanic hypoxia during the deposition of marine ooidal ironstones in the Late Cretaceous to the Early Paleogene Bakchar ironstone deposit in western Siberia; the absence of pyrite indicates oxic conditions for the remaining sequence. While goethite formed in oxic depositional condition, chamosite, pyrite and siderite represented hypoxic seawater. Euhedral pyrite crystals form through a series of transition originating from massive aggregate followed by normal and polygonal framboid. Sediments associated with goethite-chamosite ironstones, encompassing hypoxic intervals exhibit positive cerium, negative europium, and negative yttrium anomalies. Mercury anomalies, associated with the initial stages of hypoxia, correlate with global volcanic events. Redox sensitive proxies and ore mineral assemblages of deposits reflect hydrothermal activation. Rifting and global volcanism possibly induced hydrothermal convection in the sedimentary cover of western Siberia, and released iron-rich fluid and methane in coastal and shallow marine environments. This investigation, therefore, reveals a potential geological connection between Large Igneous Provinces (LIPs), marine hypoxia, rifting and the formation of ooidal ironstones in ancient West Siberian Sea.