Murky pools are small pools of water one Z-Level deep on the surface of the map. Dwarves with the fishing job active will attempt to fish in them. Murky pools can evaporate completely in summer in sufficiently hot climates, or can be drained manually, but in either case can be refilled by rainwater or melting snow or ice.
Drinking from a murky pool will give dwarves an unhappy thought. Dwarves will not normally drink from murky pools if they can at all help it; they will prefer to remain thirsty instead of drinking from a murky pool, holding out for the hope that well water or some alcohol will be produced in the mean time. However, if there are no other water sources that present themselves, dwarves will eventually force themselves to drink from a murky pool when they become very thirsty.
In order to remove a murky pool, you must first remove the water. You can do this with a pump, or you can let pools evaporate in hot/scorching climates, or you can just dig into your pools from the side and let the water drain away and evaporate.
The bottom of a murky pool will keep its "murky pool" status, presumably to let the game know that water should collect there during rain storms. You can't build certain structures, including farm plots, on dry "murky pool" tiles.
To de-murk those tiles, simply build a paved road on top of them, and then remove it. The floor covered by the road will become standard soil once the road is removed. Be aware that once you do this the tiles won't gather rainwater anymore.
A drained Murky Pool tile will block trade depot access.
Murky pools will refill with water when it rains. The degree to which they refill is limited primarily by the density of the rain itself - a brief light shower may only fill an empty pool to 2/7, while a long heavy storm could potentially refill it completely.
This effect can be used to actively generate water, which can be helpful on maps without an unlimited water supply. Create a cistern or channel some tiles next to the pool to lower its water level. Don't drain it! If you keep it at 2/7 or more, it will not evaporate (except during a dry season). When it rains, it will refill the pool and the connected cistern, increasing your supply of water.
 Preventing Evaporation
It is possible to keep murky pools from evaporating in hot weather by ordering floor tiles to be built over the pool, and then suspending the construction of those tiles. The water will not evaporate, enabling them to hold water over the hot season. Rainwater will not collect in murky pools covered this way. This may be considered an exploit.
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