Instead of dropping water from the top, pump it in from the side using the pressure to your advantage.
Let's say your drowning pit is 5x5x1 in size, on layer 20. Build a cistern a few space away that is 5x5x5, starting at layer 15 (so that the very bottom room is at layer 20, next to the drowning pit).
Make a single wide corridoor from the bottom of the cistern to the drowning chamber and put a floodgate in it somewhere and link it up so you can open it.
Fill the cistern all the way to the top with water.
Put your victims in the drowning pit. If you're dropping them from above, put a gate over the open space you can close when the pit is ready to be flooded.
Open the floodgate. The pressure from water in the cistern entering the drowning chamber will force it to fill quickly, as well as all the way to the ceiling with no air pockets. You might even get the pressure itself to just explode some of them against the opposite wall