Is depth in water a negative number?

If measuring from sea level, yes.

Technically, though, it is accurate to state depth as a negative number, but unless you have been specifically told, it shouldn't matter whether you do or not.

The only exception I can think of is if you are drawing a parabola that shows the depth of a buoyant object over a period of time after being thrown or dropped in. It looks a lot neater to show a positive parabola, as a negative parabola could imply that a non-buoyant object was thrown from the bottom of a body of water.

I hope this helped, and ignore the previous paragraph if you want.