Agriculture modern environments can vary due to factors such as land consolidation and ditch enhancement projects. But, these improvements projects can include cover-ing-up of irrigation ditches with concrete, increasing the drop between paddy field and drainage ditches, which might decrease the abundance and diversity of fish fauna around paddy fields. In this study, for the management of agrobiodiversity on fish in paddy fields, we installed a small-scale fishways between paddy fields and drainage ditches, and evaluated the effects on the eco-connection of the paddy fields, ditches and stream. Five fish species were recovered at the drainage ditches. The species exhibited characteristics spawning and growth based on the paddy field. The results indicate that the five fish species could ascend the paddy fields through the small-scale fishways. There are no difference of species numbers at ditches of environment-friendly agriculture paddy fields (A) and good agricultural practices (B) region, but individual numbers were higher at the B region. This result could be interpreted as indicating that ditch diversity was affected by positional properties rather than farming practices because the water flow and connection to adjacent stream of B region were better than A region. After ascertaining the fish species capable of ascending in a pre-survey of the drainage ditches, we set up small-scale fishways at the drop between paddy fields and drainage ditches. Three species of fish (Aphyocypris chinensis, Misgurnus anguillicaudatus, M. mizolepis) arrived at the paddy fields via small-scale fishways. The main movement time was from 18:00~24:00 and 00:00~06:00, indicating a preference for the night time period rather than the day period for migration. Concentrating the operation time from night to dawn seems prudent for effective management of small-scale fishways.