@Nikow: My fortress used single Z-level rooms. It would require quite a bit of effort to create multi level tree farms, since there generally isn't a sufficiently large soil layer between the ground and the aquifer, so you'd have to dig a multi Z-level cave in rock and muddify it it you want a high tree farm. I didn't have any foot traffic in one room, and very little in the other one so trampling wasn't an issue. I might try to create a multi level tree farm cavern in my current fortress to see if that works better. Thanks for the advice.
If multiple Z-levels are required, I don't understand the warnings about trees growing in (and blocking) your water tunnels and pumps stacks, though.
It's not soo much work as you can thins. If you will start carving your treefarm using channeling everything will be okey. I usualy have some sever system, just because i like a lot of wells (RolePlay reasons). Just dig some small room, like 3x3x1 as your tank, close it by door from one side and floodgate from other. Then pierce aquifer, so it will flood the tank room, and your dwarf fill flee by door. Later lock the door, and wall it if you do not trust your minions. Next room needs a little enginering skills: Make bigger room, like 5x5x1 with plate in middle, who will close your tank when it will be filled to 5/7 level or more. 5/7 level is safe for your dorfs, then connect it to your plumber system. Aquifer is source of infinite water and it's infinite sponge, so it will get whole water back. Good idea (sometimes) is make drain to first cave level too, just to clear it out from nasty thingies.
Small control room with levers to open/close watering system and drain is good idea.
There is other idea how to water it, i was using it when i was scared by water. Just make a 1x1x{z} holes, where {z} is your tree farm 1.3*x*y/7. Sadly, this method is slow and intense dwarve labor, because for small 10x10 farm you need 2 tubes 1x1x9 down (63 water units in each). If you want sparse your terrain, you can make smaller tubes connected to middle-section tanks, but it will waste more water units, so your dwarves will have more water to carry. The best idea is when you will make source well/water hole near your entrance above aquifer and watering tubes just near your under it. Remember, to fill 3x3 tank without evapolate you need 3z levels tube, if because you need 2/7 water on tiles, so if you use 2z level tube, not 3z, your water just disapear... after short time.
One dorf need 4 units of water/booze per season, so 3x3 tank will be enough for 15 dwarfs for one season. 5x5 will be enough for 43 dwarfs? Water is important, as you see, as reserve. But if am i correct, your dworf will carry only one unit water per bucket... And water is usesfull for engineering, like
http://dwarffortresswiki.org/index.php/DF2014:Fluid_logic#Toggle_Flipflop, just to keep autoclosing bridge closed when enemy will press plate, just because your dwarves are to slow to pull lever usualy.