When looking at ancient cities from the Near East, sometimes it's a bit overwhelming and hard to visu
Tectonic Plates
Before I dive into the geography, I think it's really interesting to take a brief look at the underlying structure. The Near East lies on an intersection of the Arabian Plate, the African plate and the Eurasian Plate.

To touch briefly on each side, in the south the African and Arabian plates are diverging (moving away from each other) giving us the Red Sea. In the east the plates are transforming (rubbing against each other) giving us the Dead Sea Transform or the Dead Sea Rift.
More relevant to this discussion, in the north, the Arabian Plate and the Eurasian plate are converging (moving towards each other at about 3cm per year) to form the Zagros Fold and Thrust Belt. The plates are coming together with the Arabian plate being forced below the Eurasian plate. The Arabian plate's being pushed down forms a depression from the Arabian sea to the Mediterranean Sea where the Euphrates and Tigris rivers lie. The Eurasian Plate's being pushed up forms the Zagros Mountains!


Now that we see the basic structure of the Near East and the kind of shapes and movements these plates are causing, let's see what the topographical and ecological effects are.
The Arabian Desert
In the middle of the Arabian continent we have the Arabian Desert, a huge, barren region of endless sand dunes.


In antiquity this acted as a physical barrier, uncrossable to most. Crossing it directly was nearly impossible until the 1st century BC when the camel was domesticated. Human travel before then was restricted to the Euphrates and the Tigris.
Farming and settlement was possible along the rivers during the winter and spring months, but come summer and autumn it became increasingly difficult.
Agriculture and Settlement
While the mountain ranges as a whole acted as a physical barrier, the steppe surrounding them was very temperate. Annually the region receives between 400mm and 800mm of rain annually which is just enough to support dry farming, a method of farming that relies on rainfall.
The map below depicts the 200mm and 400mm isohyets. Notice the 400mm line following the edge Zagros Mountains reaching all the way down to southern Levant region in the East. At 400mm dry farming is almost guaranteed to be successful!

Here we finally see our first glimpse of civilization, and we have the model to understand the reasoning behind their locations. This region, often called the Fertile Crescent, was an oasis sandwiched between harsh lands.