It has been argued by a number of literary scholars and critics that Salman Rushdie uses pollution to symbolize the censorship of free speech. This is an issue of great personal importance to Rushdie, as he was subject to death threats and forced to go into hiding after the publication of The Satanic Verses.
In Haroun and the Sea of Stories, the Oceans of the Streams of Story are so heavily polluted that Haroun's friends, the fish Goopy and Bagha, become ill. Normally, when people drink from the ocean they are transported into a completely different world, the kind of world that only stories can evoke. The ocean is a precious repository of all manner of stories, a vital storehouse of cultural memory. Yet thanks to the Chupwalas, that ocean's now become polluted by poison
The Chupwalas live in Chup, which is the land of permanent darkness. It isn't too much of a stretch to see this as an allusion to the kind of Islamic fundamentalists who've threatened—and continue to threaten—Salman Rushdie's life. The Chupwalas, just like the Islamic fundamentalists on which they're based, seek to repress and destroy any cultural traditions that challenge their restricted, narrow-minded world-view.