I am a Native English speaker (from USA).
This is something that made me think, "okay, how can I best describe this?"
Polluted - so we know the definition pertains to some kind of contamination or harmful substance.
Polluted by: think of the word "by" as pointing a finger at a person or object...Who was this water polluted by? Was it you (points finger)? Or her (points finger)? or was it the large oil company (points finger at company)?
***You don't have to point your finger, but I'm using for more animation and for better understanding.
Polluted with: the word 'with" is used to describe how the water was polluted. The water was polluted WITH plastic. The air was polluted WITH toxins. My description may have been polluted WITH poor examples=)
I hope this helps a little bit. I can give more examples, if you need.