If a water heater backdrafts, it means that potentially hazardous exhaust gases are coming back into the home. Last week I blogged about how to determine if a water heater is backdrafting; that's the easy part. The tough part is determining why it's happening and fixing it. There are many potential causes for a water heater to backdraft, so I'll cover as many as I can think of. In many cases, it's a combination of conditions.
Vent Connector Problems
A vent connector is the thing that takes the exhaust gases from the top of the water heater (draft hood) to the vent. If a vent connector isn't properly installed, the potential for the water heater to backdraft increases.
One of the most common installation defects with a vent connector is improper pitch; the vent connector need to pitch upwards towards the vent with a minimum slope of 1/4" per foot, and there should be no sags or dips.

Insufficient rise in the vent connector can contribute to backdrafting. While the code requires a minimum pitch of 1/4" per foot, if there is a quick 90 degree turn right at the top of the draft hood and the vent connector only has the minimum pitch, there's a good chance that it won't draft properly. There needs to be more of a rise created in the vent.

Most atmospherically vented water heaters come in two shapes - tall and short. Short water heaters are a couple of inches wider and nearly a foot shorter than tall water heaters. Replacing a 'tall' water heater with a 'short' gives the vent connector almost an extra foot of rise, which will increase the potential for the water heater to draft properly.
Another common defect with a vent connector is too long of a horizontal run.

The longer a vent connector runs horizontally, the greater the potential that it won't draft properly. Section 503.10.9 of the Minnesota Fuel Gas Code says that "a vent connector shall be as short as practical and the appliance located as close as practical to the chimney or vent". The photo above shows a water heater installed much farther away from the chimney opening than it should be. That water heater could certainly be moved closer to the chimney.
Another thing that can be done to help with a long horizontal run is to replace a single-wall vent connector with a Type B vent connector. This will help the vent to heat up faster, which will help with draft.