Stable isotope signatures of primary producers are known to show high inter-specific variations which are assigned to species-specific differences in isotope fractionation. Furthermore, fractionation processes can be altered by abiotic conditions e.g. pH, light, and temperature, thus increasing intra-specific variability. Since consumers reflect the isotopic signature of their food source, such variations have direct impacts on the interpretation of stable isotope data in aquatic ecology. We used a three-trophic level system in order to elucidate the variability of isotope fractionation at the primary producer level and the transfer of the signal through food webs. Strong inter-specific variations and a direct change of stable isotope enrichment in response to nutrient limitation for the different algal species were observed. The δ13C-signatures of primary and secondary consumers (copepods and larval fish) reflected only to moderate degrees the isotopic composition of their diets. The theoretical degree of enrichment of 1 δ13C and 3.5 δ15N per trophic level could only be confirmed in certain cases. The majority of isotope enrichments in the three-trophic food chain showed rather large discrepancies to the theoretical framework.