Land improvements in Japan involve the need to conserve ecosystems and biodiversity, hence research and research methods related to ecosystem conservation in rural aquatic areas are increasing and developing. Analysis in rural aquatic ecosystems using stable carbon and nitrogen isotope ratios is an important research method and such isotope ratios are used for various purposes when investigating rural ecosystems. Several characteristics of rural ecosystems have been found by stable isotope ratio analysis in Japan as described below. Food webs in drainage canals are derived from organic matter, comprising a mixture of algae and detritus attached to stones, whereas food webs in ponds originate from fallen leaves. In this study, it emerged that small food webs are sustained by various sources of materials in rural ecosystems. Quantitative results showed that most Japanese brown frogs move to secondary forests, where they feed and overwinter after metamorphosis or spawning. Micro food webs of web?building spiders differ from epigeal spiders because the carbon sources differ in terms of the secondary forest and levees, while the diversity of material flow in creatures of secondary forest ditches and the eco-tone between secondary forests and paddy fields was revealed by analyzing carbon stable isotope ratios. Analyzing stable isotope ratios in frogs indicates that frog populations include immigrants. Immigrants in reconstructed concrete canals cannot enter a new population, while the existence of immigrants in the population is evidence of dropping, washing and landing of frogs. This method can significantly boost the conservation of rural ecosystems by revealing the life processes of animals that are not well known.