The thing that complicates the use of the water saving basins, is that they tend to make the salt intrusion into the lake a lot worse [0]. So to limit the salt intrusion (through the new locks), they have to _not_ use the water saving basins, or flush the locks every now and then using a lot of fresh water from Gatun lake.

This was (and is) not as much an issue with the old locks, as passage of ships there is ridiculously fast with the use of mules. With the new locks, it's mostly tug boats, and substantially bigger/slower ships obviously.

[0] Mostly on the Agua Clara side. The Cocoli side is generally fine, as the salt wedge doesn't reach the lake. Drinking/irrigation water intakes there probably have to be (or have been) moved though.