This paper presents carbon and nitrogen isotopic results from several Swiss freshwater fish (Esox lucius, Perca fluviatilis, Barbus barbus, Rutilus rutilus and other Cyprinidae) in order to provide information about their trophic level, feeding habits and provenance. Freshwater fish remains are regularly recovered from archaeological contexts in Switzerland, which attests to the importance of these aquatic food resources to past communities. However, it can be difficult to determine the effect of freshwater fish consumption in human bone isotope signatures by stable isotope ratio analysis. Therefore, an establishment of baseline isotope signatures of freshwater fish by region and time is necessary. Additionally, freshwater fish isotope analysis can serve as a backdrop for research on former aquatic isotopic ecology. We measured carbon and nitrogen isotope ratios of 140 freshwater fish bone samples from sites dating between the 11th and 19th centuries AD. Suitable C:N ratios (2·9–3·6) were obtained from 56 of the samples, a rather low success rate that may be the result of diagenetic contamination and insufficient sample weight (<20 mg). A high inter- and intraspecies variability of freshwater fish isotope signature was observed. The δ15N results indicate a size and age-related trophic level effect. Heterogeneous carbon isotope signatures from samples from the same site could indicate spatial variation in isotope values within a single ecosystem or alternatively represent the use of different fishing grounds.