Stream restoration has been conducted in the Shibetsu River in northern Japan, which aims at the recovery of its river-floodplain ecosystem altered dramatically in the last 40 years. Well-designed monitoring before and after restoration should be conducted to evaluate the effects of the stream restoration on its ecosystem. An analysis of stable isotope ratios (δ-values) is one of the most effective methods for monitoring material cycling in river ecosystems. Because product δ-values are roughly dependent upon their source δ-values, we can trace material flows by comparing the δ-values of various compounds. In the first section of this review, we introduced a basic concept of the δ-value analysis by using an analogy from various diffusion patterns of salt water. The second section described how to calculate δ-values and discussed the difference between the analyses of natural stable isotope ratios and the tracer analyses (another powerful tool for material flow analysis). The third section presented the theoretical basis of mechanisms which change the δ-values. A product δ-value becomes different from its source δ-value in two kinds of processes: isotope exchange equilibrium and kinetic isotope fractionation. The magnitude of this difference (Δδ-value: δ_product-δ_source) tells us about the processes and activities of the reactions. The fourth section introduced specific examples from the carbon and nitrogen δ-values (δ¹³C, δ¹⁵N) of aquatic organisms to infer the degree of eutrophication and carbon recycling at ecosystem levels as well as to determine food web structures and photosynthetic activities at biological interaction levels. In the fifth section, we presented the result of our study indicating differences in food web structure between a main-stream channel and oxbow lake in the Shibetsu River watershed when their δ¹³C and δ¹⁵N values of diverse aquatic organisms were compared. The advantages and limitations of the stable isotope analysis in environmental assessment were also discussed.