I could actually see two ways you could interpret this.
The first is to make it zero and that there is no large free standing bodies of water on the planet.
The second is that the negative number represents even the scarcity of water in some other form (ice, ground water, etc.) meaning that the planet has very little water in any form on it.
This second version could make things interesting for a scenario where you need water for survival, fuel, or whatever and there's very little or none to be found in any form on a world. Now you have the players needing to come up with innovative solutions to a problem. For example you can't just drill a well since there's little ground water... There's no ice to be had anywhere... What do you do?
The UPP doesn't really allow for negative numbers, though I guess you could put a minus in amongst the numbers. I'd leave it up to the gamemaster to flesh out. Maybe it's a Mars with a wee bit of an ice-cap, or maybe what little there is is all underground and needs prospecting, or maybe it's utterly barren - any of those would be interesting. Atmosphere 0 doesn't necessarily mean it's without atmosphere either - it could all be precipitated out as ice and snow on some iceball in the outer region of the system.