Just a wild angle if you want to play with it.  You could still have your subterranean labyrinth, but rather than a sewer, the present city layers over an under city.  Probably not entirely, but there are like blocks of city, or heck it's fantasy so maybe the whole city, where the present city just build over it.  You see this in a micro level in Portland, you also see it sorta in Rochester where there was some sort of subterranean transit plan that never took on.  You got all that water down there because it's just where the water goes ... which means maybe a catastrophic sinkhole down the line, but for now a cool place where you have a literal urban underworld.  Flush or let it stand.

If you desire to stay with the realistic feel, you should find the "outfall" (the lowest point) of the sewer system where it will join your river (downstream, obviously).  Then all the other sewer elevations will have to ascend from that point back up into the city.  One feature of the system is your players can use the flow of water to figure out if they are headed N-S-E-W .  Based on the flow you can back figure what is going on.  Also, sewers that are "uphill" are always no larger and sometimes smaller than the one that leads downhill.

Now, another detail for the realism of it.  A proper ancient sewer will have a very slight V-bottom.  If for some reason, it was used as an access route for maintenance or anything else, it would have a raised 'sidewalk' along one wall or another.  The roof would be arched (round roman arches would most likely) and it would all be constructed of masonry unless it was a desert climate, where it could be constructed of timber.  In areas where they did have 'sidewalks', there would occasionally be bars across a line where people were not permitted.  In this way, people were not supposed to get access to the palace or whatever, by crawling through the sewers.  But this was only as valid as the frequency in which they were inspected.

... and yes, I am another Civil Engineer.

Quote from MusicScout >>

If you desire to stay with the realistic feel, you should find the "outfall" (the lowest point) of the sewer system where it will join your river (downstream, obviously).  Then all the other sewer elevations will have to ascend from that point back up into the city.  One feature of the system is your players can use the flow of water to figure out if they are headed N-S-E-W .  Based on the flow you can back figure what is going on.  Also, sewers that are "uphill" are always no larger and sometimes smaller than the one that leads downhill.

Now, another detail for the realism of it.  A proper ancient sewer will have a very slight V-bottom.  If for some reason, it was used as an access route for maintenance or anything else, it would have a raised 'sidewalk' along one wall or another.  The roof would be arched (round roman arches would most likely) and it would all be constructed of masonry unless it was a desert climate, where it could be constructed of timber.  In areas where they did have 'sidewalks', there would occasionally be bars across a line where people were not permitted.  In this way, people were not supposed to get access to the palace or whatever, by crawling through the sewers.  But this was only as valid as the frequency in which they were inspected.

... and yes, I am another Civil Engineer.

 Thank you! Thats some great stuff!