Rice fields are making up unique landscapes with neighbor ecosystems. However, the biodiversity in the rice paddy system has declined due to the modernization and the abandonment of cultivation as well as other causes. We evaluated the impact of these two factors affecting biodiversity in multi-scale models. In regional scale, species distribution is determined by geographical features. Land use changes affect ecological networks in a landscape scale. Finer scale modification such as land consolidation affects a local population. We focused on two important ecological networks, ecotones between two ecosystems and interspecific relationships. The distribution of the clouded salamander show a positive spatial autocorrelation. Actual distribution tended to be limited at larger habitat networks estimated by a distribution model. In a fine scale, probability of the species presence was significantly lower at modernized rice fields than traditional ones. On the other hand some plants on levee were not affected by the modernization, but strongly affected by abandonment of rice fields. We also focused on the interaction among bittering fishes, unioid mussels, and the host fishes in an irrigation ditch. The bittering fishes may be affected by irrigation-canal management indirectly through unioid mussels.