Had the same problem 20 years ago.
After I installed a between-the-studs thermostatically controlled exhaust fan in my unfinished attic to remove some of the sweltering heat build-up, I experienced the negative pressure situation others have alluded to. I could smell the water heater flue gases being drawn into the house because the exhaust fan was sucking outside air down the chimney. Nasty.
To remedy the problem, I installed an interface between the water heater and the exhaust fan, that would shut the fan down while the water heater was doing its thing.
I purchased a Fenwal Thermoswitch with specs appropriate to the temperature range I would be adjusting it for, then punched a hole in the flue pipe to accomodate insertion of the sensing tube into the flue.
The Thermoswitch is line voltage capable, but would have required running BX cable from the water heater to the attic, so I opted to use a low voltage wire run instead, utilizing a relay to handle switching of the line voltage.
When the gas fired water heater kicks in, the Thermoswitch senses the hot flue gas, and shuts the attic fan down. When the water heating is done, the flue cools off, and the attic fan comes back on.
Here's a pic of the device installed atop the water heater: