During the strongest of storms you may have water inside the water heater pan.That water may be coming from your vent system.
Water Heater vent pipes have 4 parts to them.
1)The FLASHING( the transition piece that allows the vent pipe to penetrate through the roof).
2)The VENT COLLAR (this is the donut ring around the vent and sits flushed to the flashing)
3)The VENT CAP this cap is connected at the top of the vent and keeps rain and other elements but allows the release of the water heaters hot exhaust fumes.
4) The VENT pieces. The vent connects all parts together including your water heater. It carries all the water heaters exhaust fumes outside the house.

Remember the vent pipe is exposed to hard elements like sun and wind.
The older they get the more prone to seals drying and breaking, caps getting knocked off by hard winds, birds nest and many other factors.

You should check the your water heater vent system every six months visually. A professional roofer should inspect the vent pipe after a hurricane, if a leak occurs or every 2 years.

When you hear your water alarm going off (beeping) it could be 2 things. Your heater is leaking or in most cases water coming from the vent pipe set the alarm off.
Turning the water alarm off.
By removing the sensor from the pan or removing the 9 volt battery from the speaker box will shut the alarm off.

If you have a leaky water heater our recommendation is to call a licensed plumber. Shutting down a water heater should be done at your own risk. Before you start make sure you know where the main water supply shut off is in your home, in case of an emergency.
The cold side has a shut off valve before it feeds into the water heater. Turn it off. The gas supply shut off valve should be near the bottom of the heater. Not on the heater itself but on a gas line. Turn it off
The last thing would be to release some of the pressure by turning the hot water side to a lavatory faucet on. Close it as soon as you see the stream of water minimize. This releases the pressure inside the tank and makes the leak less aggressive.
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