Stable isotope analysis is commonly used in studying flows of mass and energy through food webs and trophicrelationships in aquatic ecosystems. However, different sample processing methods can influence the measurement of these stableisotope rates, which may result in errors in the resulting food web models and the comparing results between different studies. Inparticular, errors may result from four different sources, that is, preservation, separation, acidification and dehydration. The collecttedparticulate/dissolved organic matter, bacteria, zooplankton, algae, hydrophyte, fish and zoobenthos were rinsed with deionized waterto clean off epibionts, and then stored at ?20℃. Acidification by adding 1mol/L HCl drop-by-drop was needed for carbon isotopeanalysis in samples of sediment organic matter, invertebrates with calcareous structures, and plankton. For nitrogen analysis,acidification should be avoided. Finally, dehydration was required by the analytical methods used in the determination of isotopicabundance. Both freeze-drying and drying at 40?70℃ were acceptable. In addition, materials preserved with formalin and ethanolstocks was suitable for current ecological applications of isotopic analysis and open up the possibility to reconstruct food webs andbiogeochemical changes at scales of tens or hundreds of years. In this review we summarize different sample processing prior to theanalytical determination of stable isotope ratios and the influence mechanism of some processing methods, which are fundamentalfor further methodology research.