A strongly stratified water structure and a densely populated catchment make the Baltic Sea one of the most polluted seas. Understanding its circulation pattern and time scale is essential to predict the dynamics of hypoxia, eutrophication, and pollutants. Anthropogenic 236U and 233U have been demonstrated as excellent transient tracers in oceanic studies, but unclear input history and inadequate long-term monitoring records limit their application in the Baltic Sea. From two dated Baltic sediment cores, we obtained high-resolution records of anthropogenic uranium imprints originating from three major human nuclear activities throughout the Atomic Era. Using the novel 233U/236U signature, we distinguished and quantified 236U inputs from global fallout (45.4-52.1%), Chernobyl accident (0.3-1.8%), and discharges from civil nuclear industries (46.1-54.3%) to the Baltic Sea. We estimated the total release of 233U (7-15 kg) from the atmospheric nuclear weapon testing and pinpointed the 233U peak signal in the mid-to-late 1950s as a potential time marker for the onset of the Anthropocene Epoch. This work also provides fundamental 236U data on Chernobyl accident and early discharges from civil nuclear facilities, prompting worldwide 233U-236U tracer studies. We anticipate our data to be used in a broader application in model-observation interdisciplinary research on water circulation and pollutant dynamics in the Baltic Sea.