Given Roman sophisticaton with plumbing and delivery of fresh water,
I don't see the problem of Numenorean citties handling this problem.
And there is the placing of most Middle-earth cities by rivers and/or
oceans. Gondor, Rivendell, Esgaroth, etc.
And there's the spreadout nature of less urban polities, like
Rohan and the Shire.
Now with ents I don't think disposal isues are an especial problem.
Reuse and recycle.