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[Blue_Dwarf]

I made a well by simply channeling down into an aquifer, so the well is just one tile deep and wide, and has a pile of mud at the bottom.

I remember everyone saying that it would create contaminated water (it's even on the wiki), and yet when I view buckets filled from that well it's just water (not stagnant water that I see when using murky pools).

Is it clean, or is there a hidden dirtiness property?

[Lopezruy]

There are a few bugs (Shown on wiki, somewhere.) with water. A well makes any water source, whether it be saltwater, stagnant water, etc., a drinkable type of water for your dwarves. Nothing will happen to your dwarves, except quenching their thirsts. 

[Mr S]

Caveat:  It will make the water into fresh, drinkable water, but it will NOT remove any contaminants from said water.

Many a fortress has had a vampire impaled in its well to make a vampire multiplier.

[Blue_Dwarf]

Clarification: even without a constructed well the water looks clean. Meaning a simple hole in the sand 

Is that the expected behaviour?

[Mageziya]

Water drawn from a one z-level thick well will be laced with mud. This is only important when dealing with hospitals.

To avoid this, have minimally a cistern/hole that is filled with water at least 2 z-levels thick. The top layer amount doesn't matter, just as long as there are at least 2 layers.

[Wurgel]

Clarification: even without a constructed well the water looks clean. Meaning a simple hole in the sand 

Is that the expected behaviour?

why not? Sand is extremly good at filtering water.

[Loud Whispers]

To avoid this, have minimally a cistern/hole that is filled with water at least 2 z-levels thick. The top layer amount doesn't matter, just as long as there are at least 2 layers.

The brilliant thing being you can use this to make a clean well drawing water from the aquifer.

[Zivilin]

I was wondering about the same thing. I think this picture visualizes the issue:

Spoiler: Aquifer vs Murky Pool (click to show/hide)

The bottom screen shows the bottom of a Murky Pool. It says that it is full of "Stagnant Water", and I think it is reasonable to assume that a well built over this tile would provide stagnant water, thus causing unhappy thoughts for any dwarf drinking it etc.

The top screen shows a single tile of channeled aquifer. The tile is said to contain only "Water", and a dusting of mud. Is this as bad as having stagnant water? Back in v0.31.25 I also used multilevel-cisterns under wells to have clean water, but I always filled them either from a Murky pool or a river. Th Well Guide wiki article from v0.31.25 seems to imply that a single tile channeled into aquifer provides clean water. Did this change in v0.34?

[Akura]

I don't believe water laced with mud provides the same unhappy thought as drinking stagnant water.

Best bet would be to use a screw pump to move the water into a constructed cistern. I don't think screw pumps moves contaminants through them.

[Blue_Dwarf]

Is "Water laced with mud" something you can read somewhere?

I'm confused because I don't see it anywhere, not in the water hole, not in the bucket description, not on the water description itself. All I see is "Water[10]", which suggests clean water.

In older game versions, I do somewhat remember seeing "Water laced with mud" though.

[GreatWyrmGold]

There are a few bugs (Shown on wiki, somewhere.) with water. A well makes any water source, whether it be saltwater, stagnant water, etc., a drinkable type of water for your dwarves. Nothing will happen to your dwarves, except quenching their thirsts. 

Last I checked, it just made dwarves ignore the saltiness.

[Sutremaine]

Is "Water laced with mud" something you can read somewhere?

It should be visible in the description of the bucket.