The role of agriculture waterways as a habitat for aquatic plants after farmland consolidation has not been recognized. The goal of this study was to clarify how concrete agricultural waterways contribute to regional plant diversity and to elucidate factors that determine the distribution of aquatic plants in such waterways. We compared the aquatic flora in an irrigation canal, drainage canal, marsh, river, and rice field in a farming region in Northern Japan. The drainage had the highest ratio of uncommon species among the five habitats, and raised regional β-diversity. The analysis of environmental factors showed that aquatic plants could become established in the concrete waterway provided the current was less than 0.25 m/s during the irrigation period. The emergent and the free-floating plants were distributed throughout areas with low dissolved oxygen (DO) and pH. The floating-leaved Potamogeton species were distributed throughout the main drainage canal, which was characterized by high DO and pH. A specific habitat in which rare plant species dominated, characterized by the inflow of spring water, low current and high water temperature, was established in some sections of the lateral drainage canal. It is concluded that consolidated drainage canals are extremely important for conserving regional plant diversity. In addition, this study showed that various drainage types, various current and oxygen conditions, inflow of spring water, are important for maintaining aquatic plant diversity.