Organic nitrogen is an important part of the nitrogen cycle in oceans, with both particulate and dissolved forms serving as substrates for bacterial growth. Proteins are the principal organic nitrogen compounds of living biomass and therefore believed to be very labile; however, some portion can be found in dissolved organic matter pools. Experimental incubations were used to examine the structural modification and degradation of the model protein bovine serum albumin (BSA) in different aquatic environments. Size-exclusion chromatography along with amino acid analysis and electrospray ionization mass spectrometry showed that high molecular weight material formed over the time course of the incubation was resistant to degradation. Low molecular weight products were formed from sequential hydrolysis, with the selective removal of polar, charged amino acids and were rapidly utilized by the bacteria present. As degradation of the protein products progressed, the amino acid composition shifted back towards the original protein composition.