Shifts in tissue nitrogen isotope composition may be a more sensitive general indicator of stress than measurement of high-turnover defensive biomolecules such as metallothionein and glutathione. As a physical resource transmitted along the trophic web, perturbations in protein nitrogen metabolism may also help resolve issues concerning the effects of contaminants on organisms and their consequential hierarchical linkages in ecotoxicology. Snowy egret nestlings (Egretta thula) fed mercury-contaminated diets of constant nitrogen isotope composition exhibited increased relative delta15N values in whole liver (p = 0.0011) and the acid-soluble fraction (ASF) of the liver (p = 0.0005) when compared to nestlings fed a reference diet. When nitrogen isotope data were adjusted for the source term of the diet, liver mercury concentrations corresponded with both whole liver relative 15N enrichment (r2 = 0.79, slope 0.009, p < 0.0001) and relative 15N enrichment in the acid-soluble fraction of the liver (r2 = 0.85, slope 0.026, p < 0.0001). Meanwhile, significant differences were not observed in hepatic levels of the metal-binding peptides metallothionein and glutathione despite a nearly 3-fold difference in liver mercury content. Because increases in tissue delta15N values result from increased rates of protein breakdown relative to synthesis, we propose that the increased relative liver delta15N values reflect a shift in protein metabolism. The relationship between ASF and mercury was significantly stronger (p < 0.0001) than that for whole liver, suggesting that the relationship is driven by an increase in bodily derived amino acids in the acid-soluble, free amino acid pool.