If there are pollutants in air they will be in the water, but it's not a actually a problem because, although they might be bad to breath, most air pollutants are harmless when eaten.

Carbon (soot), Ozone, NOs, sulfur dioxide (smog), etc are harmless to eat.

I'd imagine it'd have to do with the digestive ecosystem, if there were any that worked that way.

But if there were it would be something that requires acid or digestion to "activate". Or perhaps something that can't be absorbed without something the only exists in the gut.

Bacteria actually could do that. Inhaled they would rapidly die, but in the gut they could live (more food for them) and cause illness.

Also, the gut will absorb things faster than the lungs. So I could easily imagine a toxin that has little effect when inhaled (since it's absorbed too slow to cause damage) but causes trouble when eaten (everything is absorbed at once).

But I don't know of any specifically.

Any air that distills out water that was worse to drink than what was available locally would probably kill you to breathe just as quickly.