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Global climatic and palaeogeographical changes generated a siliciclastic–carbonate system with high organic matter accumulations in a shallow sea during the lower Permian in Western Gondwana. The 60 m thick mixed siliciclastic–carbonate succession (Irati Formation and the base of the Serra Alta Formation) from the Paraná Basin represents a singular record of the interplay between carbonate production and siliciclastic input, providing a window of opportunity to integrate large‐scale depositional architecture with facies and geochemical analyses. The detailed study of cores supported by outcrop columnar sections revealed a siliciclastic‐dominated, retrogradational to aggradational facies, and a carbonate‐dominated, mixed aggradational to progradational facies composing three depositional sequences that record an outer‐ramp and mid to upper‐ramp. An integrated approach based on the description of facies and microfacies, organic geochemistry and mineralogical composition, indicated high‐frequency palaeoenvironmental changes during the evolution of this restricted basin. Climate changes, resulting in humid and dry phases, produced ideal conditions for high organic matter production and dolomite formation. The high organic matter production (humid phases) in addition to the restricted condition was responsible for the anoxic bottom waters that were widespread due to the low angle and homoclinal platform. Nutrient‐rich freshwater inflows in the anoxic and hypersaline restricted basin created a density‐stratified water column causing low‐salinity surface and anoxic bottom water, which allowed planktonic life, typical of lakes, such Botryococcus braunii, to flourish in the photic zone and sulphur bacteria to populate below the chemocline. Microbial activity induced primary dolomite precipitation (dry phases) and widespread formation of synsedimentary dolostone. Freshwater inflow and marine incursions are reflected in the organic matter accumulation (kerogen types I and II, respectively), generating bituminous shale with high total organic carbon (5 to 27 wt.%). [ABSTRACT FROM AUTHOR]