Most fantasy cities are pitched at a level of technical advancement that has mage's academies and temples analogous to universities in our world. These have often been established for a very long time, there is always some artificial reason why technology has not advanced that much, the timeline moves on a lot slower than earth. By the time a place has universities, it is well on the way to having the tools to fix its filth problem. Maybe the cities have had their versions of Joseph Bazalgette design a way to fix it.
One a side note...
One of my favourite PCs and later NPC was a Wizard who was a Water Elementalist and was the city's leading sanitation worker. He was university educated and had grand plans for aqueducts, clean water supplies and irrigation systems. He had a fanatical devotion to improving the world through clean water. He had to go adventuring to make the money to prototype his ideas in order to get funding from the university and government. Many of his adventures were related to clearing blockages in the sewers, often caused by slimes, monsters, smugglers, cultists and bandits.
He ended up with a pet ooze, which ate all organic matter. He used it as a water filtration system, installing it in water systems, he pumped sewerage in to feed it and it expelled fresh clean water. It grew HUGE and needed its own containment area, almost like a nuclear reactor, he was always afraid of it going free. He made a pet of sorts of an Otyguh too, anything that feeds on filth is actually a very cleanly thing to have around, the more it eats the cleaner a place gets.
One a side note...
One of my favourite PCs and later NPC was a Wizard who was a Water Elementalist and was the city's leading sanitation worker. He was university educated and had grand plans for aqueducts, clean water supplies and irrigation systems. He had a fanatical devotion to improving the world through clean water. He had to go adventuring to make the money to prototype his ideas in order to get funding from the university and government. Many of his adventures were related to clearing blockages in the sewers, often caused by slimes, monsters, smugglers, cultists and bandits.
He ended up with a pet ooze, which ate all organic matter. He used it as a water filtration system, installing it in water systems, he pumped sewerage in to feed it and it expelled fresh clean water. It grew HUGE and needed its own containment area, almost like a nuclear reactor, he was always afraid of it going free. He made a pet of sorts of an Otyguh too, anything that feeds on filth is actually a very cleanly thing to have around, the more it eats the cleaner a place gets.