Stable nitrogen isotopes (delta N-15) are used as indicators of trophic position (TP) of consumers. Deriving TP from delta N-15 of individual amino acids (AAs) is becoming popular in ecological studies, because of lower uncertainty than TP based on bulk delta N-15 (TPbulk). This method would also facilitate biomagnification studies provided that isotope fractionation is unaffected by toxic exposure. We compared TPAA and TPbulk estimates for a sediment-dwelling bivalve from two coastal sites, a pristine and a contaminated. Chemical analysis of PCB levels in mussels, sediments, and pore water confirmed the expected difference between sites. Both methods, but in particular the TPAA underestimated the actual TP of bivalves. Using error propagation, the total uncertainty related to the analytical precision and assumptions in the TP calculations was found to be similar between the two methods. Interestingly, the significantly higher intercept for the regression between T-AA, and TPbulk in the contaminated site compared to the pristine site indicates a higher deamination rate due to detoxification as a result of chronic exposure and a higher N-15 fractionation. Hence, there is a need for controlled experiments on assumptions underlying amino acid-specific stable isotope methods in food web and bimagnification studies.