I am double posting due to the different construction and all the text I predict it will take.
The new water-treatment-system is much more user friendly. It is however untested and not guaranteed to work.
The key here is quite simply: Pumps and nurses. While that sounds incredibly sexy, it is not what you think ... I am going to describe the construction for you and then add a question mark or two.
The idea is that you shouldn't have to micro-manage this stuff. So the dwarves have to be self reliant. It also assumes that the dwarf knows how to swim, since he will be submerged in water.
There are a series of rooms that need to go into this:
First the water supply. Ideally it should be fresh water, taken from a river and running -benath- the room and continuing on into a chasm or whatever. The reason is simple, the nurse is going to drink from this water and it cannot go stale. To risk evaporation and to manually have to refill it through buckets is a no-go. To build this room -above- a river could work too, as the water can easily flow back into it.
Second the power supply. The construction should be close to the surface, partially because of the easy access to water, and because of the windmill. I am not experienced with any power BUT windmill and manual power, so this is the only design I can make. The windmill should power the pumps at all times, it needs to be 100% automatic.
Third the pumps and the patient room. The pumps should be located in a relatively large room, where the patient room is actually just a canal going through the middle. It's pretty straight-forward but a couple of things need to be considered: The entry pump should flow the water in a tunnel before going into the canal, there should be walls to prevent splatter, mudforming and "dangerous terrain" cancellations on the sides of the canal beginning. There should also be a well for the nurse to drink from. The idea is that the exit pump should be located directly above the nursing bed. So the patient gets flooded while in bed but the water pump takes it away, so the nurse can stand right next to him and feed him without being in water ("dangerous terrain") herself.
NOTICE I am unsure if a dwarf is willing to put a patient in a bed that's being flooded, so if the dwarf is washed out of bed - he might stay out of bed. For this reason an emergency lever connected to the gear assembly under the windmill has to be made, as well as drainage grate located in the canal right after the patient bed. With this construction, you can easily turn the whole system off and put the dwarf back in bed.
Fourth the nurse's office. It's not easy being a nurse, the dwarf who takes this job must enjoy helping others to prevent negative thoughts from forming when performing her duties. She will be completely isolated from the fort, to keep her happy she should have an office and a dining room - and something she likes. (wonderful creature in a cage, perhaps) This is perhaps unneccessary if she has no friends, but if she has friends - and orcs bust their nuts - she's going to need comfort. Also note that the nurse's office should have a separate bedroom with a door connected to it - this is to prevent the wounded dwarf from wandering in there, if he ever gets blasted out of bed. You might need to put a door in the canal too, if he is a repeat offender. This, sadly, means micro managing alot.
Fifth the farm and food stockpile. Another reason to build the construction close to the surface, with natural earth you don't need to artificially irrigate the stone floor to farm, you can do it right off the bat. For this reason the nurse should be a planter and the farm should be huge - don't be afraid to make multiple farms so she can keep busy planting multiple seeds, it'll only keep her happy. Though I don't think she will actually harvest them unless there is a stockpile nearby. The stockpile should obviously be allowed to hold seeds as well. There needs to be a channel in the roof, in which your other dwarves can throw down extra seeds if she needs them. And booze if you're feeling generous. Again, this is cause for micromanagement but the construction should be able to be virtually self-sustainable.
NOTICE 2 It is best to place the drainage grate after the door, so that if the dwarf is blown out of bed - he hits a locked door. Instead of land on the grate where he won't be sufficiently submerged in water.
NOTICE 3 I haven't tried out the pumps, so the most important question is this. WILL the dwarf really be submerged when he is in front of the pump? Or does the water disappear so quickly that it doesn't count? If so, can the nurse stand in front of the pump without getting the "dangerous terrain" ? If not, maybe one has to double a pump AND floor grate, if that works. and the nurse wants to use the space, maybe one has to find some way of lessening the water strength to keep the patient from being thrown out of bed all the time ... since he can't be in front of the pump anymore he has to be in the canal where the waterlevel is high and the flow is strong.
Edit: the reason that the nurse is to be separated from the fort is because the whole room should be locked. patients have a nasty tendency to get out of bed and run to the other end of the fort to sleep in some barracks