Unfortunately I didn't retain any saves from before the flooding, so some backstory:
I had tunneled into a mountain lake from below, to get water from my well - all other sources had dried up. The lake was level with my main fort, so I built an access tunnel for the digging from two levels above - pressure forced water up one of those levels. I also dug another level down just to the right of this access - my well was fed through this tunnel. Obviously it would've flooded, thus there was a floodgate to cut off the water supply.
After I finally dug into the lake, this happened:
- My miner ran for his life, ahead of surging water
- A giant toad got sucked in and got bruised - yay!
- Water surged *even faster* through the lowest tunnel, into the tiny well chamber, and out of the well
- I pulled a lever, dropping the floodgate and stopping the flood. It dried up fairly quickly.
So far, so good, but the seeds of disaster had apparently already been laid. I don't know if this would have happened had I stopped touching it, but regardless, a little later I decided to drain the well chamber (by digging into it from the side) and install a pressure plate to control the floodgate. Thus:
- Drain channel was dug. Well drained.
- Pressure plate installed, but the floodgate was still underwater - odd, since the water there *should* have been forced into the well chamber by pressure; moreover, there was still a 7/7 square on the stairway above the floodgate.
- Time passed. Not much time, but some. Eventually, and apparently spontaneously, the well chamber started flooding again - and didn't stop, flooding my kitchen too but not flowin upwards.
- I saved, copied the save, then made a movie of my various attempts to fix it - the last one successful.
You can find the savegame and (long) movie at http://brage.info/~svein/df/ .
Although I successfully stopped the flood, I'll be reverting to the save to see if I can figure out exactly what caused it, and what stopped it. I'll be replying here if I do.