Kumamoto City has been known as the “Water City” since ancient times, and it has also earned the title “Japan's Number 1 Groundwater City” because 100% of the water used by all 740,000 residents is supplied entirely by groundwater. Previously, the city implemented various measures to protect water quality by monitoring wastewater from industries and purifying groundwater polluted by organochlorides. However, in recent years, there has been an increasing trend of nitrate nitrogen in groundwater in the eastern and central parts of the city, and creating countermeasures for this problem has become an urgent issue. In order to preserve the quality of groundwater for future generations, the city began to implement countermeasures against nitrate nitrogen pollution by establishing the Kumamoto City Tobu Compost Center in order to properly treat domesticated animal manure, which is the main cause of nitrate nitrogen pollution in the eastern part of the city. Countermeasures will continue to be developed against nitrate nitrogen pollution through cooperation among citizens, private cattle farmers, and municipal governments.