Similar to .40d then. Just use a deep cistern with a floodgate. Connect it to some persistent water source, and dummyproof with a floodgate on the intake. Calculate total fluid volume of the cistern using its dimensions to allow a close to 50-50 mix of 1 and 2 deep water in the growing chamber.
This allows you to refill the cistern from the inlet, and once full, it is primed to perfectly re-mud the room without flooding the fortress.
(say for instance, you have a grow chamber that is 10x10, or max farm plot size. You want your cistern to contain as close to exactly 150 water as possible (perfect mix of 1 and 2 deep water when completely flooded). You want your cistern to be multiple Z deep, so you have pressure to rapidly fill the grow chamber when the floodgate is opened, so you want each level of the cistern to contain approx 75 water, and be 2z deep. The closest perfect (and square) number, using 7 depth water in each level of the cistern, is a 3x3 room. This gives us 63 water per level, or 126 water total, which is enough to fill the grow chamber to a mixture of approx 75% 1 deep, and 25% 2 deep water every time.)
So, something like this:
Z-1
O---O
(water source) |XXX|
|---------> FXXX|
|XXX|
O---O
Z-2
O----------O
| |
| |
| |
O---O |
|XXX| O-------------------
|XXXF (GROW) D L L (To Fortress -->)
|XXX| (ROOM) O-------------------
O---O |
| |
| |
O----------O
Where F are floodgates, D is door, and L are levers to control the floodgates.
This could be adapted to be a multi-purpose setup: Since each cistern is 2Z deep, each can be used to ALSO supply a single well from the floor above the waterworks level, while having the cisterns be connected to a communal water intake pipeline controlled by the dummy shutoff floodgate. The additional water stored in the pipe network between growing chambers would just get us closer to the "Ideal" mix of 50-50 1 and 2 deep water per chamber. (current single cistern design is a little dry, but sufficient.) We could have a whole network of small cisterns, feeding several growing chambers, all controlled by 2 levers. First lever controls the master shutoff from the water intake source, and the second throws open all the grow chamber floodgates at once. This totally drains all cisterns into their respective grow chambers, and empties the pipe network. We empty all the cisterns at once, so that water in the connecting pipes is distributed evenly between all chambers, instead of flooding one in excess of 2 deep water on accident.
In this way, we could have a hospital in the floor above, for instance.
With the "200 max seeds of each type crop" limit, and with "Limited to underground crops only" restriction imposed by no soil tiles, and thus no surface plant availability-- we would need AT MOST 8 such grow chambers. We could not operate more than that, and that is assuming 100% utilization on all possible crops. (If we accept having some rooms only run half the year, we could run maybe 2 more than that, making very seasonal crops like rock nuts.) To get more than that (and it is hard to imagine needing more than the output yeild from that with skilled farmers!) you would need to use herbalism on a massively excavated room that you regularly flood, and allow to grow moss (and wild underground plants).
It would be easier to use underground lakes for such a secondary project. The primary one could be accomplished with some murky pools I think.