Found a large puddle in the kitchen this evening. Water was dripping from the flue atop my water heater. I thought the air conditioner line had split, but it's disconnected, and the problem persists. Whenever I turn the water on, it drips. When I turn it off, it stops. The water heater has been off for about three hours now. How would water get into the flue in the first place? Please help. No hot water or air conditioning until I get this fixed.

When the gas is burned it produces CO2 and water, mainly, along with some acids and a little carbon monoxide, depending on how well the air is mixed with the gas before burning. If a lot of water is coming out of the flue it could mean that you have a pinhole water leak that is producing steam and condensing in the flue pipe. I have never seen this happen before. You could also have a water pipe leak near the flue pipe and the water is hitting the flue pipe and going where you have found it. You need to look more carefully at this problem and get in attic and check the pipes and the flue. That much condensate from burning gas is pretty much impossible.

Could be rain running down from a leaking weather boot.