Stable isotope analysis has become a standard tool in bioaccumulation and biomagnification studies, because it can provide trophic position estimates for a consumer in a food web. This enables calculation of trophic magnification factors for environmental contaminants. There are several major uncertainties, however, associated with the use of isotopes in ecology and, particularly in ecotoxicology. Exposure to contaminants may lead to profound changes in stable isotope fractionation via alterations in metabolic pathways involving protein synthesis and tissue turnover. Consequently, altered protein synthesis in an organism may lead to an apparent elevated trophic position, but not as a result of a diet change but rather as a response to contaminant exposure. Compound-specific stable isotope analysis (CSIA) can help in confirming the lack of diet change in stressed animals from field samples. Fractionation in bulk δ15N is due to large increases in the δ15N of some amino acids (AA) and little or no change in essential AA. Hence, AA from a single sample can provide information about both trophic level, and nitrogen sources at the base of the food web, and the difference between essential and non-essential AAs can be used as an internal index to more precisely quantify trophic position or, as we propose here, stress.