Carbonation can always lead to excess acid as can lots of other things and when many people experience the result of that which it is most noticeable is during sleep. You definitely sound to have GERD and the carbonated water isn't helping.
However, if you drink it really early and stop 5 or so hours before bed time, I wouldn't think it would affect you. How's the rest of your diet? Often losing weight, not eating much the hours before you go to bed, etc. will help reduce acid reflux.