the consistency, density, and shear weight of the water is different than the other substance. That is why Walt kept telling them to WAIT until they disconnected. Walt is a brilliant chemist and a very calculating person (in regards to science). He knew what he was doing.
methylamine is less dense than water, so it essentially forms an organic layer ON TOP of the water.
Walt was telling them to wait because he wanted to hit exactly 1000gallons. Yet there was no measure of how much water was going back into the tank..
I'm trying to understand the scientific basis behind this.. To say a fictional character "knows what he's doing" is hardly reason for me to accept it..