I have a State Select 50 gal. direct vent, gas water heater, model # PR650NBRT. It was installed when the house was built in 2002. It supplies two bathrooms and is located in the attic directly above both of them. Whenever one of the showers is in use a loud "growling" noise comes from the water heater. It almost sounds like a hammer banging from the inside. I can hear it from the bedrooms of the baths supplied by the heater. I have been in the attic, next to the water heater, when it makes the noise. No vibrating input or outlet pipes and no leaking anywhere.
Anyone have any ideas of what this could be? I've been ignoring it since it started several months ago, but am wondering if it is a symptom of a serious problem.

Thanks in advance for any help offered.

One thing this could be is that a layer of deposits have settled to the bottom of your heater and as your heater starts to heat the small amount of water that is trapped under this "rock" on the bottom overheats and turns to steam and releases steam bubbles that burst loose and come to the top of the heater, usually this makes a rumbling noise along with some pretty sharp pops as the steam is released.
One way I have found to quieten down this noise is to turn the fire down a bit, not the thermostat but the actual burner itself. This could slow the recovery rate but it is well worth the noise reduction.

One other thing, when your heater is hot and has full water pressure on it and a faucet is opened somewhere in the house that reduces the water pressure in the water heater by a couple of pounds, and could be more depending on the piping and such. But like a steam cooker, the when the pressure drops the water boils, that could be what is happening in your heater.