Hydrostatic pressure means that all the water above your living area will wind up in your living area. Which means that if you cut off the water at the start of the aqueduct, you still get entire aqueducts volume.
Moreover due to some quirks of the simulation, on each sim cycle you will get a tile full of water out for each pair of vertically adjacent water tiles, which explains why things may have occured more suddenly that expected
Side view
time 1 time 2
#~~~~# # #
#~~~~# #~~~~#
####~# ####~#~~~~
####~~~#### ####~~~####
########### ###########
Actually, probably faster than shown here (due to the drops in the down shaft), but you get the idea
I got like 6 floors down
Your ascii art was a bit hard to interpret but it looks like you were attempting a vertical diagonal.
What you actually need is a horizontal diagonal, eg
Top view
##~##
##~##
##~##
#~#~#
##~##
##~##
##~##
Pressure will not travel North/South through this. Someday Toady will fix this and there will much wailing and gnashing of teeth (although it will be somewhat muted due to, you know, being underwater and all)
You were already able to shut the water off at the source, right? It shouldn't be too hard to drain the place.
Option 1:
1 Dig a shaft to the caverns.
2 Make sure that this shaft will not flood your remaining area (doors, hatches, depressurizers, all-of-the-above...)
3 Connect the shaft to the flooded area.
4 Don't forget to reseal the shaft sometime between when things dry out and when some flying abomination uses the shaft to make a surprise visit. (You may want to consider the benefits of grates and fortifications during step 1)
Option 2:
1 Dig out an area below the flood
2 Build an atomsmasher down there
3 Make sure not to flood your remaining area
4 Connect the flooded area to the atomsmasher and crush water till its out of the areas you want access to.