Yeah, see the EDIT i made before.
I made river first and then reed the whole description of the city

The image is still a reference for the hills that made the city the shape Zweitholou projected. Of course it may be a cliff as well. Of the old Dwarven quarry maybe?
If there was a river, the local quarries, which reach so deep, would probably have huge problems with leaking water. Also the undercity caves would most likely be submerged... although it should make Klyros happy, to have water right away, 1-5 meters under their houses.
I would like to make few points on some of the city description details.
The wall, 3m wide and 7 high if i remember right... Thats a huge wall, explains why the quarries are so big.... But they must have been building them over 300 years or something, meaning that the newest city part is 300 years old at least and since then nothing changed :o.
I propose that 2m wide and 4m tall wall was only around the upper quarter and the rest of the city have 0,5-1m wide, 2m tall wall with wooden scaffold where the wall is 0,5m. Is it acceptable in any way?
The Rockcliff quarry dome.
with 500m diameter? :o The only way how i see it, is to project it like bridges,
Brooklyn Bridge its longets span is nearly 500m and the human built it in 1883 year. If you really want it, I'd say it is the biggest child of the Xacha enginery i have ever heard.