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[Virvatuli]

I built a cistern directly above my stagnant river to get a source of fresh water. I started to pump water from the river into the cistern, and to my surprise, the water I pumped up was also stagnant. The cistern has never had any water in it before. Is this perhaps due to the cistern being above the river, ie some of its tiles sharing x and y coordinates with tiles in the stagnant river, or shouldn't that matter? What else could have gone wrong?

[slowpokez]

I'm not an expert on the subject but maybe your cistern is dirty?
For me that's usually the problem

[Virvatuli]

What do you mean by dirty? It was free from contaminents (no blood, mud etc.), it was empty as far as I could see. It was also constructed by stone blocks if that matters at all.

[Sphalerite]

Something strange is going on with stagnant water in the latest release.  Tiles are becoming stagnant merely by being somewhat near stagnant water tiles on the same map.  It's been reported in the bug tracker:

http://www.bay12games.com/dwarves/mantisbt/view.php?id=5232

[GhostDwemer]

Try making a cistern away from the river and let us know what happens. Stagnant water is an area of ongoing research. I think your guess may be right, as the well is technically above a stagnant source.

[Virvatuli]

Oh, then it's probably a bug. Just wanted it confirmed. Thanks Sphalerite for the link!