I've had trouble with this as well. My solution was to wall off my pool into 4-by-4 (1 deep) cells and fill those with water using the "endless well" technique of emptying a water bucket into two opposite corners.
Once you've filled every cell, you can start breaking down the walls between the cells one block at a time. Sometimes the same effect that makes the endless well work will fill the removed block fully. Sometimes it won't. If it doesn't, empty a bucket directly onto the space.
For pools more than one block deep, completely fill the bottom layer and then build the cell network for the next higher level "suspended" over your filled layer and continue the process.
Repeat ad infinitum. Obviously this takes a lot of time and effort.
Of course in your case, since you just have one "little" problem area (compared to the total area of your pool), try walling off just that area, removing the water, and trying my method above, destroying the outer walls last.
The key is to remember that water in a bucket is a block just like everything else.