I’ll just answer this real quick because I’m in a pretty modern city where this was poorly designed. The tunnels don’t technically mix, but the stormwater drains are designed to overflow into the sewers if they breach capacity in a storm. Then you get sewage flooding into the streets, into the rivers, into the lake…
And this is a major city in a first-world country, mind you, designed less than two hundred years ago.
Depends on the quality of the system. Some go straight into waterways, resulting in some of the most polluted waterways on Earth. Some small ones run into underground septic systems or biological greywater systems, which don’t really ‘go’ anywhere. Some run for miles to a water treatment plant.
Subways, maintenance tunnels, natural cave systems (if you have limestone bedrock), basements of condemned buildings, sewers, stormwater systems, overflow/backup tunnels, aquaducts in really ancient cities, catacombs, tombs, mines, tunnels for any cable/pipe/other linear system that needs monitoring and maintenance, old parking garages (if applicable), cellar systems, ventilation systems, geothermal air ducts, underpasses for people or wildlife, escape tunnels (some old mansions have them), tunnels intentionally connecting buildings… I could probably go on, but that’s probably enough, hey?