As Japan underwent changes in the political realm at the end of the Nineteenth century, further industrialized and increased its integration in global exchanges, the ecological cost of this transformation provoked long-term conflicts between industrialists, rulers and the affected local population. This article analyses the example of the pollution incident caused by the Ashio copper mine, one of the country’s worst pre-war cases of river contamination. This case study depicts how scientific knowledge was weaponized by the Japanese government to impose the acceptance of the side effects of industrialization on the population, emphasizing the political dimensions of the administration over water bodies.