How can you have a right to clean water if there is no clean water near you? Do other people have to come give it to you?
Do you have the right to air unpolluted "unnaturally" (i.e. excl. passing gas) by your neighbors?
Not in my opinion. You do have the right to not be harmed by others, but when it comes to shared resources like that, you're going to have to agree as a society on what is acceptable and what isn't.
What about smoking in close proximity to others?
Still not infringing on a right, but it's something I think should be against the rules of any society. Rights are fairly black and white. "Close proximity" is gray.
Do you think naturally occurring fresh water should not be considered a shared resource, "owned" by the citizens of the country in which the water is found?
It should be considered a resource shared by every being on the planet. It's impractical to consider polluting water an act that requires the consent of everyone whose "right" would be infringed, which is why I don't think it's meaningful to call it a right. Pollution must happen. Societies should determine the extent to which it should be allowed and who should have a say.