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[GhostDwemer]

I've got an underground cistern that draws from an underground lake through a pump. The lake is two z levels deep. Although not connected to the edges at the surface, the deeper parts do connect to the edge. Oddly, the lake refills slowly, and even more oddly, the only tiles that permanently decrease in depth are those with underground trees in them. Now I have a lake with mostly 7/7 water, except for a few patches with depths of 5 and 6 where the trees are. Anyone else notice that tree filled tiles don't seem to refill correctly?

[Sphalerite]

Yes.  This happens because trees block the flow of water in and out of a tile.  Saplings can grow underwater, but can't mature into trees if the water is 7/7 deep.  Underground lakes tend to have saplings grow up underwater, but never mature into trees.  When you start draining water from the lake you start having spots in the lake with water less than 7/7 deep.  The moment one of those saplings has less than 7/7 water in its tile, it matures into a tree.  The 5/7 or 6/7 of water in that tile is trapped there, because trees block the flow of water, and even when the lake refills that tile will never fill because water can't flow into it.

[Stoup]

I had this phenomenon occur to me when trying to dig my fortress's first well. Presumably when the well was used for the first time, it lowered the water level in the tile for just a moment, which was enough for a tree to grow right at the base of the well. Annoyingly enough, this prevented the well from being used... and I couldn't very well go down there and drain the lake just to chop that one bloody tree down.

So! What I decided to do was to deconstruct the well, dig a z-level above it, and collapse a section of the cavern onto it.

Since I forgot about the suction effect of falling cave sections, this caused the miner who dug the tile to fall to his untimely death. First death of a dwarf in my fortress, and how improbable a death it was...

[Aspgren]

Yes.  This happens because trees block the flow of water in and out of a tile.  Saplings can grow underwater, but can't mature into trees if the water is 7/7 deep.  Underground lakes tend to have saplings grow up underwater, but never mature into trees.  When you start draining water from the lake you start having spots in the lake with water less than 7/7 deep.  The moment one of those saplings has less than 7/7 water in its tile, it matures into a tree.  The 5/7 or 6/7 of water in that tile is trapped there, because trees block the flow of water, and even when the lake refills that tile will never fill because water can't flow into it.

It's the worst when they spring up in a canal and cause floods. 

[hjd_uk]

Ive had this block dug/constructed water channels before, water leaved mud, spores seed the mud, bloody tree grows in my stone-channel with constantly flowing water. I seriously wish you could protect sections from this.

Can plants grow on muddy Paved Roads?

[Sphalerite]

Any building or construction - including roads or constructed floors - will prevent plants from growing.

[Reelyanoob]

Exploit: I've found that saplings won't mature on any square with a designated stockpile on them, so you can designate all you waterways as stockpiles (custom, turn off all categories) and they never block. Advantages of this is it takes no dwarf time to do or resources, gives a consistent look to the waterways, and if you are really short on wood you can clear the channel,  temporarily delete the stockpiles, and the mature saplings instantly "pop" to full size for harvesting.

[andyman564]

plants can't grow on ramps (natural or artificial). if you have the extra z level for channeling, this is a very easy way to construct plant proof waterways.

P.S. you may want to floor over the channel to prevent water related FUN.