In nitrogen uptake studies with N-15 tracer techniques, a common observation is that the N-15 label added at the start of the experiment is not fully recovered at the end of the experiment in the particulate and dissolved N pools measured. We have made direct measurements of the N-15 content of the traditionally measured NH4+ and particulate N pools, as well as the dissolved organic N (DON) and bacterial pools in studies conducted in Chesapeake Bay, the Caribbean Sea, and the Choptank River (a subestuary of Chesapeake Bay). We found that the fate of the ''missing N-15 differs from eutrophic to oligotrophic waters and is dependent on the length of incubation, the dissolved inorganic N substrate used, and the length of time the sample was contained before the N-15 uptake experiment. In general, it appears that it is more important to include the N-15 that enters the DON and bacterial pools to achieve a N-15 mass balance in more oligotrophic ecosystems and when longer (> 1 h) incubations are used.