It might make it go alkaline, but that's not the same as the water having a negative magnetic "charge". There's no such thing. All magnets have to poles. So, even if you could magnetise water, it would be both positive and negative. Every magnet has two poles. It's the only way.
Possibly the magnets induce some sort of ionisation in the water.
Sounds interesting though. I've been wanting a cheap and easy way to alkanise water.