We evaluated the potential utility of stable isotope analysis of tissues commonly archived by aquatic biologists. Previous studies with chemically preserved samples have shown contradictory results, which present an obstacle for the use of archived sample materials. We tested the effects of ethanol and formalin preservation on zooplankton and of ethanol on benthic macroinvertebrate δ¹³C and δ¹⁵N values. We found that neither formalin nor ethanol had a significant effect on δ¹³C and δ¹⁵N values of preserved zooplankton. Nor did ethanol significantly affect δ¹³C or δ¹⁵N values of macroinvertebrates. However, ethanol preservation slightly, but significantly decreased C:N ratios of both zooplankton and macroinvertebrates, probably reflecting some extraction of lipids. Overall, the effects of preservatives on δ¹³C and δ¹⁵N values that we observed were minor. We also compared δ¹³C and δ¹⁵N values analysed from roach scales and perch operculum bones with those analysed from muscle tissue. Decalcification of scales and operculum bones only slightly improved our comparison to muscle tissue δ¹³C and δ¹⁵N values. Decalcified scales had slightly higher δ¹³C and lower δ¹⁵N values. Similarly, decalcified operculum bones showed slightly increased δ¹³C and decreased δ¹⁵N values to those for fish muscle. Our results confirm that scales and operculum bones can provide a suitable proxy for fish muscle in isotope studies with minor correction. We conclude that various archived sample materials can indeed be used with confidence for historical reconstructions of freshwater food webs by stable isotope analysis.