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[Faeryx]

So I have been attempting in my last few fortresses to set up wells, and I cannot figure out how to do so the the water is not muddy, because I think the 'dusting of mud' is making water drawn from the well stagnant. When I check buckets it says 'stagnant' water. Most of my attempts have just been opening a hole in the side of a brook or river, but there is no way for me to get the water so that it doesn't touch at least one dirt/sand/clay square so it always ends up muddy. Any suggestions?

[Fusty]

Only the bottom tiles in a pool will be muddy.  If you fill your pool up to 2+ levels you will ensure the bucket only dips into the clean top layer. 

Who wants to drink from the bottom of the well anyway, blech!

[i2amroy]

Only the bottom tiles in a pool will be muddy.  If you fill your pool up to 2+ levels you will ensure the bucket only dips into the clean top layer.

This. And it's the fact that there is water touching the ground (not necessarily dirt or sand, any ground at all), that makes it muddy. You could have mud in an entirely constructed stone reservoir if it was the bottom layer of said reservoir.

[Faeryx]

Alright, so why is that when I use K and Enter on the bucket the water is stagnant? Or is because they are taking water from the murky pools and I just don't see it....?

[Sphalerite]

Mud and stagnant water are not the same thing.

Water always deposits mud on any surface it travels over.  It does not matter if the water is fresh, stagnant, or salty.  You can't prevent this.  You can stop buckets from picking up any of the mud by making the water under the well at least two Z-levels deep.  Only the bottom layer will have mud in it, so water taken from the layers above that will not be muddy.

Stagnant water seems to behave similar to salty water, in that if a tile has ever had stagnant water in it, any water that is ever placed in that tile will become stagnant.  Stagnant water also seems to spread like salt water, in that if any part of a body of water is stagnant, the entire thing will be stagnant.  Furthermore, it is likely that all the water on your site is stagnant.

The reliable way to make a source of fresh, clean water is to build an above-ground cistern, making sure none of the tiles of the cistern have ever had stagnant or salt water in them, and fill it via one or more pumps.  Make the cistern two or more Z-levels high and wells built over it should always give clean, fresh, non-muddy, and non-stagnant water.

[Faeryx]

The way I set up the well was by digging out a tunnel, that did not at any point have stagnant water touching it and letting water flow out of a river to fill the tunnel, then I constructed a well over it so I don't see why the water would be stagnant.

[Sphalerite]

The river water may have been stagnant to begin with.  Have you tried constructing a well directly over the river and seeing if that generates stagnant water?

[Faeryx]

Why would the river water be stagnant?

[Sphalerite]

Why would the river water be stagnant?

Because Dwarf Fortress laughs at your logic and real-world-based expectations.

[Loud Whispers]

Why would the river water be stagnant?

Because Dwarf Fortress laughs at your logic and real-world-based expectations.

Or if it had areas of slow moving water.
<sub>I'll just go out this door...

AND ENTER THROUGH ANOTHER DOOR OH YEAH</sub>

[albatross]

Indeed. With pumps you can purify water. It's the only sure-fire way. Just like someone said elsewhere, stagnant or salty water spreads like electricity - any pure water it touches turn instantly into stagnant or salty water, including entire rivers or brooks, permanently. So be careful. Build a pool/cistern, then pump water into it.