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The transition from the Middle to Late Ordovician cold climate to the Silurian greenhouse phase was marked by major climatic and oceanographic changes. The vast epereic sea that during the early Paleozoic extended over the Baltic Plate for hundreds of kilometres recorded the dynamic processes that characterized this important climatic evolution. This shallow epicontinental sea experienced phases of hypoxic conditions for millions of years during the Silurian favouring the sedimentation of organic-rich deposits. A continuous core drilled in the Silurian fine-grained succession of the Baltic Basin was studied integrating sedimentological, palynological and geochemical data. The succession, deposited in a restricted environment in low-energy settings, recorded three long-term variations in bottom-water redox conditions. Our data highlight a direct control of long-term climatic changes on oceanic redox cycles. Phases of cool and dry climate with reduced runoff altemated with periods of warmer and humid conditions with higher runoff and fluvial discharge. During warmer and more humid climatic phases, the presence of a stable pycnocline hampered deep-water renewal efficiency, and together with increased nutrients led by enhanced weathering and runoff favoured the onset of anoxic bottom-water conditions. Cooler and drier intervals favoured instead a weaker and less stable pycnocline that, coupled with more oligotrophic conditions, drove the formation of oxic bottom-waters. The variation through time in water salinity and temperature influenced both the type of organic matter in the surface waters as well as its preservation along the water column. In fact, the extended residence time at the stable pycnocline during the anoxic phases led to the degradation of the organic matter and limited its accumulation at the sediment-water interface. The waning of the latest Ordovician cooling to the Silurian greenhouse climate was characterized by the progressive altemation of cool phases and warmer periods. The effect of this dynamic climatic instability on the redox state of the Baltica epicontinental sea protracted over millions of years up to the middle Silurian.