Nowadays, it has become very common to find in Japan that nitrate nitrogen concentrations are very high in spring water and in well water where the land use of a watershed is agricultural. We have often observed around 50 mg/L of nitrate nitrogen in the spring water where we live. Crops produced in those fields are mainly vegetables such as celery, cabbage, lettuce, carrots, and so on. Green tea is also popular in Japan. In order to produce good quality green tea, farmers apply a great amount of nitrogen fertilizer. This amount can reach up to 1,000 kg/ha in some areas, although the average application amounts to 628 kg/ha in Japan. As a result, ground water that is rich in nitrate flows into the river, which results in a high nitrogen concentration in river water and ground water. Further, this causes a low pH in river water in some tributary rivers in Japan, though this kind of case is very rare. We knew from field tests that if water contained a high nitrogen concentration and was introduced into paddy fields, high nitrogen removal would be performed. This paper presents the outline and results of a system on how to remove nitrogen using paddy fields (wetlands). Further, this paper presents the evaluated results of the removal quantity at the watershed level.