Japan doesn't have near the pollution problem that most of the world has. They are known for being a very clean, pollution-free country. But there is pollution in Japan. Their air quality is horrible though, despite the fact that there isn't much litter waste in the country. Some years back, the country suffered from widespread mercury poisoning in the air. They are a huge consumer of fossil fuels and also use a lot of it which goes right into the air and into the people's lungs and bodies. The Meiji period was the time in which many Japanese were ill due to the pollution in the air.
The Yellow River is also full of pollutants. So, while the country looks to be very clean, it is very polluted. The industrialization of Japan has take its toll on the enviornment. Being the leader in importing renewable and exhaustible natural resources. there's really no way around the fact that they would also be a leading contributer to pollution in the air and in the water. While the country is nothing like India or China with trash everywhere, it is still a huge contributer to pollution that you really can't see but you can definitely feel.