We present an application of multi-isotopic fingerprints (i.e., 236U/238U, 233U/236U, 236U/129I and 129I/127I) for the discovery of previously unrecognized sources of anthropogenic radioactivity. Our data indicate a source of reactor 236U in the Baltic Sea in addition to inputs from the two European reprocessing plants and global fallout. This additional reactor 236U may come from unreported discharges from Swedish nuclear research facilities as supported by high 236U levels in sediment nearby Studsvik, or from accidental leakages of spent nuclear fuel disposed on the Baltic seafloor, either reported or unreported. Such leakages would indicate problems with the radiological safety of seafloor disposal, and may be accompanied by releases of other radionuclides. The results demonstrate the high sensitivity of multi-isotopic tracer systems, especially the 233U/236U signature, to distinguish environmental emissions of unrevealed radioactive releases for nuclear safeguards, emergency preparedness and environmental tracer studies.