Amino acids (AAs) comprise a large fraction of organic nitrogen (N) in plankton and sedimenting matter. Aquatic studies of organic N compounds in general and of AAs in particular, mostly concentrate on marine environments. In order to study the cycling and fate of organic N and AAs in lakes, we measured the N isotopic composition (d15N) of bulk organic matter (OM) and of single hydrolysable AAs in sediment trap and sediment samples from two Swiss lakes with contrasting trophic state: Lake Brienz, an oligotrophic lake with an oxic water column, and Lake Zug a eutrophic, meromictic lake. We also mea- sured the N isotopic composition of water column nitrate, the likely inorganic N source during biosynthesis in both lakes. The d15N–AA patterns found for the sediment trap material were consistent with published d15N–AA data for marine plankton. The AA composition and primary d15N–AA signatures are preserved until burial in the sediments. During early sedimentary diagenesis, the d15N values of single AAs appear to increase, exceeding those of the bulk OM. This increase in d15N–AA is paralleled by a decreased contribution of AAs to the total OM pool with progressed degradation, suggesting preferential AA degradation associated with a significant N isotope fractionation. Indicators for trophic level based on d15N–AAs were deter- mined, for the first time in lacustrine systems. In our samples, the trophic AAs were generally enriched in 15N compared to source AAs and higher trophic d15N–AA values in Lake Zug were consistent with a higher trophic level of the bulk biomass compared to Lake Brienz. Especially the difference between average trophic d15N–AAs and average source d15N–AAs was sensitive to the trophic states of the two lakes. A proxy for total heterotrophic AA re-synthesis (RV), which is strongly asso- ciated with heterotrophic microbial reworking of the OM, was calculated based on d15N values of trophic AAs. Higher RV in Lake Brienz indicate enhanced heterotrophic bacterial reworking of AAs under oligotrophic conditions. Despite changes in the d15N–AA values within the sediments, the proxies based on these values were consistent over the studied sediment profile, indicating the preservation of trophic signatures; therefore, our results underscore that d15N–AA analysis of sedimentary records represents a promising tool to assess trophic levels and bacterial re-synthesis in lakes.