How would you know where an aquifer is?
When you're choosing where to embark to. One of the windows shows what the top seven levels are made of, roughly. Cliffs and such can change this. It also shows if there's an aquifier on each of those levels. For example:
Peat
Sand
Red sand *****
Granite *****
Marble
Granite
Slate
The ***** is the game's symbol for water. Which would mean that the third and fourth levels, the red sand and the first granite, have aquifiers in them.
But the aquifiers are like other terrain features, meaning they have set areas when the map is generated. If you move the embark area around on the map, you can choose which portions to include in it. Like a volcano or portion of a river. Except you can't see exactly where an aquifier is, the game just telling you that there's an aquifier in your embark area. So if you start with no aquifer shown, move the embark area up one, and it shows one, you know that at least one of the top squares of your embark area has an aquifier, but the lower ones don't. You just have to move the area around to pinpoint where it is.