Proteins are the principal organic nitrogen-containing compounds of living biomass and by virtue of the readily cleaved amide bonds are believed to be very labile. Nevertheless, proteins have been found in multiple organic matter pools. Experimental incubations among three diverse estuarine environments (anoxic Chesapeake Bay, Lower Delaware Bay, and freshwater marsh) were used to examine the initial stages of protein hydrolysis and associated structural modification and degradation of the model protein bovine serum albumin (BSA). Size-exclusion chromatography combined with electrospray ionization mass spectrometry observed multiple proteinaceous products of lower molecular weight formed over the course of the incubation. Products ranged from 63 to 13 kDa, suggesting initial degradation via sequential hydrolysis. Complete hydrolysis of added protein occurred in all three environments within 48 h. Amino acid analysis of the intermediate products of degradation suggests that the initial process (hours) involves the selective removal of polar, charged amino acids by bacterial assemblages present. As degradation of the protein products continues, other functional groups are lost, leaving the overall amino acid composition of remaining material closely resembling that seen for the intact protein.