Although it is believed that water pollution was an issue in Japan before its industrial modernization, the first major recorded case of water pollution affecting the population occurred at the turn of the century, during Japan's Meiji Period (1868-1912), when waste dumped into the Watarase River by the Ashio Copper Mine poisoned local residents. Subsequently, the environmental impact of Japan's continued industrialization made water pollution an increasingly serious issue, with a many incidents of water pollution affecting areas throughout Japan.

During the postwar reconstruction following WWII, water pollution became a more serious issue, due especially to urbanization. Toward the mid-1950s, water pollution began creating ecological disasters, including the infamous Minamata Disease, which was a case of mercury poisoning in southwestern Kyushu.
Local governments began responding to the issue by establishing their own water-pollution regulations. The national government also began to act, in 1958 establishing two laws regulating water pollution: the Water Quality Control Law and the Industrial Effluent Control Law. But these two laws didn't do enough to curb water pollution, and further were restricted in scope to specific regions. They were thus unable to answer the demand for environmental protection of Japan's water.

Japan's rapid economic growth during the 1960s was accompanied by water pollution of increasing severity and scope. This period saw one ecological disaster after another, including Minamata Disease, caused by mercury contamination in the Agano River, and Itai-Itai Disease, caused by cadmium contamination in the Jinzu River. Itai-Itai Disease was so called because the cadmium made patients' bones so brittle that just touching them would cause them to cry out "Itai! Itai!" (It hurts! It hurts!) This prompted the national government to take stronger measures to curb water pollution. In 1967, it enacted the Basic Law for Environmental Pollution Control, and then in 1970, the Parliament passed a number of pioneering anti-pollution laws. In fact, it passed so many such laws that it was nicknamed the "Environmental Pollution Diet." The Parliament unified the Water Quality Control Law and the Industrial Effluent Control Law into a new and strengthened law, the Water Pollution Control Law. Then the following year, in 1971, the Environment Agency was established, which took over water-environment policy in order to provide centralized oversight for environmental conservation.

Nevertheless, during the 1970s environmental pollution became an increasingly serious issue around the Seto Inland Sea, due to overpopulation and growing concentration of industry. One consequence of this pollution was increasingly frequent red tides. The government responded with tougher measures to curb water pollution. In 1973, the Interim Law for Conservation of the Environment of the Seto Inland Sea was enacted, and in 1978, the law was made permanent and the term "Interim" dropped. Also in 1978, a comprehensive and far-reaching series of laws was enacted to regulate levels of pollutants in the Seto Inland Sea, Tokyo Bay, Ise Bay, and other bodies of water, where organic pollutants were a recurring issue. Then in 1984, the Law Concerning Special Measures for the Preservation of Lake Water Quality was enacted to combat water pollution in freshwater bodies, where measures to date had failed to show results.

In recent years, pollution has failed to show improvement in closed bodies of water such as bays, inland seas, and lakes and reservoirs. Further, chemical pollution is becoming an increasingly serious issue. In response, in 1989 the Water Pollution Control Law was revised to prevent the pollution of the water tables by toxic substances, and in 1990, it was revised again to strengthen measures against pollution from sewage. Then in 1993, a series of standards was enacted to prevent further chemical pollution of public waters. Environmental Quality Standards (EQS) relating to human health were greatly enhanced and strengthened, and additionally environmental quality and wastewater standards were enacted to prevent eutrophication and nitrification of sea and coastal areas, with 23 substances specified for monitoring. Then in 1996, the Water Pollution Control Law was again amended, incorporating measures to clean up groundwater pollution, and the following year (1997), Environmental Quality Standards (EQS) were established for groundwater pollution.

Emissions of dioxins from waste incinerators became a major public issue in 1998. In response to the problem, the Law Concerning Special Measures Against Dioxins was enacted in July 1999, and environmental quality and effluent control standards were established based on the new law. Regulations controlling dioxin emissions in wastewater became effective in January of the following year (2000), and water quality (including groundwater) and soils have been observed regularly since April 2000.

By 2002, there was an increasing movement toward regulating soil pollution. The attitude of the public toward ground pollution was changing, as awareness of the need for regulation grew as a result of increasing discoveries of soil pollution and soil pollution countermeasures. Based on these circumstances, the government planned out a strategy for combating soil pollution, and in February 2002, the Prime Minister's cabinet approved a new policy. In May of that year, the Soil Pollution Control Law was passed by the Parliament, and went into effect on February 15, 2003.

Today, the issues affecting the water environment are more serious than ever, and as we have seen here, the measures to combat them go back many years. In January 2001, the Environment Agency was reorganized in to the Ministry of the Environment. This represents one more step in Japan's long battle against water pollution. The Ministry's stance is described in the following section.