Actually (yes, I said it) the Nile is very much not there anymore. in fact, Asani lives where the Nile once used to flow.
one working theory that isn't canon but might become it (it's not definite yet), is that a big part of that water has found a new path underground, which is what fuels the scarce water pits that people use to collect water from.
You could say it is possible that Zeta and Adira are located where they are located because they sit on top of underwater basins that formed with the falling of the Nile through the cracks of a breaking earth.
again, theory crafting that might never become definite canon, to explain at least in part the survival of people in what has been for a long time a toxic wasteland. Zones are not a reliable source of raw material or special items on which to build a civilisation on... and Cairo itself is mostly a toxic place, which is why only Decayed thrive there.
Water is a highly prized resource. In fact, the Thermae are more a power move than a simple relaxation space. The queen shows her absolute power and wealth by essentially wasting a lot of water.
If you look at it hard enough, the economic structure that sustains Zeta and its surrounding falls to pieces very quickly. We handwave a fair bit of it, and what we don't handwave either remains in the background or is expressed in very broad terms that would not hold up to scrutiny (but then, neither do 400 year old car batteries).