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[Libash_Thunderhead]

I want to clean the water using this method.

Strange thing is, it worked earlier today when I played vanilla df but doesn't work this time.  The designs are almost identical. I'm using PeridexisErrant's Starter Pack with dfhack default settings this time.

Basically I just add a screw pump over a channel and build a windmill above the pump. I'm puzzled because the second time both sides have stagnant water, while the first time it produced clean water.

[anewaname]

If you use the "pause the game and use . to advance by one tick" method, and you check the water blobs that shoot out of the screw pump, before they fall into the second pond, are those blobs water or stagnant water?

[PatrikLundell]

If you use the "pause the game and use . to advance by one tick" method, and you check the water blobs that shoot out of the screw pump, before they fall into the second pond, are those blobs water or stagnant water?

Most probably not. As sort of indicated by the question, sending clean water onto contaminated tiles (such as e.g. murky pool ones) will recontaminate the water. A murky pool floor can be "demurkified" by building a floor over it, and the murky property is gone as you remove the floor (over = on top of the ground, not at surface level one Z level up). I suspect you'll also get rid of it by making a dirt road over the murky pool bottom, but haven't tried. Note that destroying the murky pool property also destroys the ability to collect rain water.

[Libash_Thunderhead]

I didn't know the floor trick. Thanks.
Do I have to cover the entire pool with floors?

[Libash_Thunderhead]

I rechecked the save in which this method worked, and found all the water in the murky pools became clean.

Wow, maybe it is not the pump but something else? I'm now really confused.

Maybe the clean water "infested" the stagnant water and they all became clean? But the source pools are 1 z level above the pump, it doesn't make sense.

[Saiko Kila]

Maybe the clean water "infested" the stagnant water and they all became clean?

This is possible. There were many problems with contamination of this kind, so it was reworked that natural cleaning is possible. This was actually long time ago (v0.34.09, "Stopped salt from spreading to fresh water, made fresh water destroy stagnant water"), but I believe there were minor fixes to this later.

[PatrikLundell]

I don't know if you need to destroy all murky pool tiles in a pool to get rid of stagnant water, or if the stagnant property stays in the murky tiles. However, I'd rather channel out my own pool rather than rework a murky one.