Off the top of my head: the aboleth had expanded the sewer to form his lake. The original sewers themselves are tiny, cramped, and traversing them requires wading through the muck. Basically an intentional subversion of the spacious sewers of fiction.

Creatures encountered might include mephits (Ooze or Water), a Basilisk (petrification would likely block the channel), and Gibbering Mouthers. If they're still outside the city, consider some environmental hazards---the sewer can be shallow, wide, and open to the air, resulting in slow water but deep muck, quicksand and dead vegetation (and predators lurking in the vegetation. Maybe they find a corpse, if you need a plot hook).

To keep it from being an incredibly linear dungeon crawl, allow various shortcuts. Let them climb out through storm-drains to bypass sections, although their stench may attract unwanted notice, if relevant. At least some unused sections should be high and dry. Possibly erosion will have worn new channels. The walls may be weak, and easily widened. If they have access to Water Breathing, make sure they stumble into other, completely submerged channels, possibly containing more dangerous, organized foes, or simply pockets of accumulated poisonous air.