This study reconstructs the depositional conditions of ironstones within the Chulym-Yenisey basin and assesses the iron source. The detrital minerals of the studied deposits include quartz and feldspar. The authigenic minerals are goethite, siderite, aragonite, dolomite, calcite, apatite, barite, and pyrite. The clay components include minerals of the chlorite group (possible chamosite), nontronite, kaolinite, illite, and beidellite. Local bacterial sulfate reduction led to the formation of pyrite framboids in siltstone layers. The subsequent diagenetic iron reduction promoted the formation of chamosite from siderite. The goethite precipitation occurred in an oxidic aqueous environment. The Cretaceous continental sediments of the Ilek and Kia Formations of the Chulym-Yenisei depression consist of fine- and medium-grained, cross-stratified, poorly sorted litho-feldspatho-quartzose sandstones of fluvial channel origin alternating with bluish-gray siltstones and ironstones of floodplain–lacustrine–bog origin. Thin layers of iron-bearing rocks within siltstones formed in meromictic waters. The changes in geochemical proxies demonstrate fluctuations of paleoenvironmental conditions within the Cretaceous sequence. Siltstones and sandstones formed under humid and arid conditions, respectively. The primary iron source for sediments of the Chulym-Yenisey depression was determined as volcanogenic and igneous rocks of the Altai-Sayan mountainous region.