We present the first application of multi-isotopic fingerprints (i.e., 236U/238U, 233U/236U, 236U/129I and 129I/127I) for the discovery of unrevealed radioactive sources. Our data indicate that, besides the reactor signature from the two European reprocessing plants and global fallout signature, there must be a previously undiscovered additional reactor 236U source in the Baltic Sea. This reactor 236U may come from unreported discharges from nuclear research facilities in Sweden, or it may come from accidental leakage from disposal of spent nuclear fuel on the Baltic seafloor, either reported or unreported. Such leakage would indicate potential problems with the safety of seafloor disposal, and may be accompanied by leakage of other radionuclides. The results demonstrate the high sensitivity of the multi-isotopic tracer systems, especially the newly accessible 233U/236U signature, to distinguish environmental emissions of unrevealed historical or present radioactive releases for nuclear safeguard and emergency preparedness, as well as tracing environmental processes from the releasing sites.