The only enemies in the sewers, up until the last part (four guards) are rats, which do not count towards Clean Hands and Ghost, so you can be a little more noisy than usual. Beware of the packs of rats infesting the sewers; if they decide to feast on Corvo, they will swarm you, attack, and possibly kill you.

Rats count if the action is caused by you, if they are behind a door and you let them out whatever they do is on you. Even random rats will count against you if you've interacted with the character, whether it be combat or knocking them out.