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Aquifier
An aquifer is a subterrainean layer of water-bearing rock. Attempts to mine through them will result in the mined-out squares immediately filling with water, effectively halting excavation at or below their level. This, in conjunction with the fact that they are often located in areas rich in clay, loam, and sand, makes it difficult to find great quantities of stone in areas with aquifers, making for more challenging gameplay.
Dealing with Aquifers
The challenges presented by an aquifer may be circumvented in several ways. Firstly, much more of your equipment will likely be made from wood, especially early on, so it may help to be in a heavily forested area. Once you've established your fortress a bit, you will also be able to trade for stone and metals if you run short.
It is also worth noting that it is by no means impossible to find stone on these maps, it is simply much rarer. It may help to create exploratory shafts searching for pockets of stone. Be aware that mining along the level immediately above the aquifer will result in patches of 'damp stone,' which will flood if mined out; these squares will flash with water when designating mining areas.
Finally, it may also be possible to pump water out of an area flooded by an aquifer. (Experiments so far haven't been successful, but I may be doing it wrong, as I'm still figuring out how to work with pumps and power. -Abbalah) If the aquifer's z-level can be accessed via pumping or other means, it is often rich in porous stone.
Advantages of Aquifers
It's worth noting that the presence of an aquifer, while challenging, does offer some slight advantages. Firstly, much of the area underground but above the aquifer will be sand, clay, or loam, all of which can be planted in without requiring any kind of irrigation or flooding, allowing farming to get under way quicker and more easily. Additionally, the presence of water 3-4 z-levels below ground anywhere on the map makes placing wells a simpler task, as well as ensuring easy access to subterrainean water supplies.