Water heater backdrafts are caused by vent connector problems, vent and chimney problems and insufficient combustion. If the water heater in the house is backdrafting, that means potentially harmful gases are coming into the home.
Improper installation of a vent connector will contribute greatly to the potential the water heater has to backdraft. A common defect in vent installation is improper pitch. There shouldn't be any sags or dips in the vent connector and it should pitch upward at least 1/4" per foot. A horizontal run that's too long is another defect in vent connector installation and will disrupt the draft. One can replace the single wall vent with a Type B vent connector.
If a chimney or vent becomes obstructed in any way, it could cause backdrafting. One can prevent this by installing a cap at the exterior vent terminal. This will prevent debris from collecting as well as thwart downdrafts caused by strong winds.
Water heaters require plenty of air for combustion. Bathroom and kitchen exhaust fans have the potential to pull enough air out of the house to make the water heater backdraft. Try closing all windows and doors, run only exhaust fans and the water heater. If it backdrafts in this situation, open a few windows or a door and see what happens. If after this test, the heater drafts properly, that means there is insufficient combustion.