Quite simple actually. The supplier knows how much water it puts in the pipes, and consumers have meters that measure how much water they take out of the pipes.
Water is water... It doesn't matter if you're not getting the exact same water molecules put in by your supplier.
Think of it like this... You have a jug of water. The supplier puts in a glass of water, and you (the consumer) take out one glass of water. The quantity of water in the jug stays the same, but you pay the supplier for how much water you took out.