This study on harbor seal (Phoca vitulina) pups of the North Sea evaluated concentrations of 14 essential and non-essential elements (Al, As, Be, Ca, Cd, Cr, Fe, Mn, Mo, Ni, Pb, Se, Sn, and Zn) in whole blood samples. The essential elements are analyzed to give references for health status determinations of pups. The measurement of classic toxic metals, like Pb or Cd, and other elements that may be in toxic concentrations in blood, is important due to their influence on health, particularly on the immune system. Blood samples of six seal pups found on the German Wadden Sea coast of Schleswig-Holstein in 2004 and transported to the Seal Centre Friedrichskoog, Germany were collected. The blood sampling was performed three times, immediately after collection of the newborns, after 1.5 months, and after 2 months before their release back into the wild. Inductively coupled plasma mass spectrometry and total reflection X-ray fluorescence spectrometry were used to determine the element concentrations. We found higher concentrations of Al, As, Fe, Mo, and Zn in blood samples of newborns compared to samples collected later, probably due to transplacental and lactational transfer from mother to fetus. Furthermore, there is a high need for, in particular, Fe and Zn in the developing organism, which may cause reduced values after some month. In contrast, the concentrations of Be, Cd, Ca, Cr, Pb, Mn, Ni, Se, and Sn, which were low in newborns and increased during the study, may be due to the fish fed to infant pups. Compared to free-ranging adults, in pups, the concentrations of Al, Ni, and Pb were higher in contrast to lower concentrations of As, Mn, and Mo. This case study is the first report on element levels in harbor seal pups of the North Sea.