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[DaComputerNerd]

I read that drawbridges will not close in certain situations, such as when there is a really heavy thing on it. However, in the application that I was using them for, there was no heavy creatures. I was using it to control water. There was a little bit of mud, as well. However, when the pressure plate should have sealed the drawbridge as it had before, at 5/7, it didn't. End result, my whole fortress flooded out of the well. Why did it not close? What else should I keep in mind for things that can stop a drawbridge?

[DaComputerNerd]

Alternatively, perhaps it messed up the plate? What can stop a pressure plate from working?

[Fleeting Frames]

Well, first of all, pressure plates don't work properly when set to trigger on 0-0 water.

Second, mind that pressure plates don't send "toggle" - they send "Open" when they're triggered, and "Close" 99 steps after trigger is removed - if trigger is never removed or added back before then, this is never used. Unintuitively, drawbridges raise on "Open" and lower on "Close".

Third, a drawbridge - any building with delay on signal, really - will ignore further signals if it is already reacting to the previous one. With pressure plates, this can happen for raise-lower cycle if the trigger is present for but a single step - a minecart coming off a valid ramp is typical use, with the result of drawbridge either raising or lowering, but not both.

Fourth, if you accidentally marked drawbridge for deconstruction (and then unmarked it), it will temporarily turn it into a third state, where it acts like a workshop impassable tile, allowing water/minecarts/projectiles but not dwarves to pass and generating implied floor if there's none present, otherwise taking floor it is built on for material/track guiding. To reset it to previous state, the drawbridge will have to be lowered, and then raised again.

[Loci]

Third, a drawbridge - any building with delay on signal, really - will ignore further signals if it is already reacting to the previous one. With pressure plates, this can happen if the trigger is present for but a single step - a minecart coming off a valid ramp is typical use, with the result of drawbridge either raising or lowering, but not both.

While the window for an Open -> Close transition to overlap requires a single-tick trigger, the window for a Close -> Open transition to overlap is much larger (anywhere from 1 - 99 ticks).

That's very likely to be the cause of OP's woes: the pressure plate had 4/7 water for 99 ticks causing the plate to send a Close signal to let in more water. At some point in the next 99 ticks a tile of 5/7 water randomly flowed across the plate causing it to send an Open signal which the bridge ignored. The bridge then finished lowering, flooding the fortress and ensuring the pressure plate remained above 5/7 water so it was never reset to send another Open signal.

End result, my whole fortress flooded out of the well. Why did it not close?

Any system that requires signalling to not flood your fortress is a disaster waiting to happen. Here's a plan that uses 0 moving parts and, properly constructed, cannot possibly flood your fort.

[Fleeting Frames]

Ah, right. Right you are, thanks for correction. Edited "if trigger is never removed" to "if trigger is never removed or added back before then" (relevant for lot of repeaters) as well as marking it to be about raise-lower cycle in particular.

[DaComputerNerd]

The plate was set to 5-7 water. So basically, it simply toggled too fast for the drawbridge, so the raising signal was lost, water flowed in, and it never raised because the water kept it in that range. I think a solution is a second plate set to open at a higher level, so that if the first is missed, water can flow in and trigger the second to close it before floods occur.

[Fleeting Frames]

Or set the plate farther in (provided the water isn't pressurized). If you have ^╬7~ setup, I imagine the 10 units of water is going to fill it up pretty fast.

Alternate solution is to use a delay or relay, i.e. ^X^╬7~, though in this schematic the floodgate will remain perpetually open after the first time unless water is drained from it's tile.

So might want to use small minecart setup elsewhere as delay, i.e. minimally like this:
z1 ¢/⎕ (R)oute (S)top with minecart placed on it, set to do nothing.
z0 ^/= track/plate. (Yes the track is necessary.)

Hatches(and doors) cannot get signals too fast, so even with ^╬7~Pressure it should work (though pressure flood-fills through all available space, so you'll still flood your fortress to an extent). A dwarf will come and place the minecart back on hatch after it has closed to reset the system.

[DaComputerNerd]

Since I had the space and was on the same z-layer as the river it is filling from, I simply set the second pressure plate further back, with 1 more on the minimum to trigger it.