The Water Framework Directive (WFD) requires member states to implement a strategy to meet the environmental quality standards (EQS) set by the WFD for a number of priority substances. Since the EQSs listed in the WFD are derived to protect the most sensitive species in the ecosystem, often top predators or humans, it has been decided that for certain priority substances the quality standards should be compared to a monitoring species with a trophic position (TP) similar to the diet of the most sensitive species. To enable such adjustment require both knowledge about the monitoring species TP in the food web as well as the relationship between contaminant concentration and trophic position. In this study, we focus on finding a suitable method for TP estimates of perch in Swedish lakes by evaluating both traditional stable isotope analysis in bulk samples (BSIA) using different baseline matrices and the more recent development of compound-specific stable isotope analysis in amino acids (CSIA-AA). For this, three representative monitoring lakes were selected in which perch together with potential baseline matrices (bivalves, gastropods and sediment) were sampled. We applied triple-isotope analyses, d15N, d13C and d34S, of bulk material of all sampled matrices, and in addition d15N in perch using CSIA-AA. Results showed that TP estimates derived from CSIA-AA were significantly (p<0.001) lower compared to all the BSIA-derived methods and further that the BSIA-derived TP estimates using gastropods as a baseline were significantly higher (p<0.001) than all other TP estimates. Since no statistical differences could be detected between TP estimates based on bivalves, sediment or a ‘mixture’ baseline these were assumed to produce similar results and therefore all valid baseline matrices for TP estimates of perch in these three lakes. In the present study we also attempted to adjust mercury contaminant data to a specific TP of 3.5 according to the WFD. The adjustment resulted in significantly different concentration for one of the two tested lakes but did not influence the chemical status classification as all lakes were well above the threshold for mercury in freshwater lakes.