The consequences of nutrient loss (oligotrophication) and attendant low productivity on biodiversity and productivity in the ecosystem has recently invoked the interest of researchers, as result of loss of wild anadromous fish by acceleration of urbanization and deterioration of natural riparian ecosystem such as dam construction, habitat destruction, and artificial hatchery program. In Japan, chum salmon (Oncorhynchus keta) have been mass-produced by hatchery program, while numerous wild Pacific salmon have been almost extinguished by a combination of the urbanization and the deterioration of riparian ecosystem. This review focuses on effects of anadromous fish on biodiversity and productivity in the riparian ecosystem with relation to dynamics of nutrient, biofilm, aquatic insects, salmonids, terrestrial animals, and human activity, and isotopic evidence for enrichment of salmon-derived nutrients. Anadromous fish are key species for sustaining production and biodiversity in the riparian ecosystem. For sustainable conservation management of riparian ecosystem, the rehabilitations of wild salmon population, system of material cycle, and natural rivers are critical important issues in Japan.