Depending on whether it is gas or electric, it may not be correctable. Changing elements on an electric heater will cure it for a time, but a gas heater gets mineral buildup on the center flue and those deposits will cause a popping sound. Draining the water will not help, but there could be a different cause of the noise which would be apparent were we to hear the noise.: My water heater is making a noise like something is boiling in it with rocks. I just placed in a water softner and I do not know why the boiler is making noise. It was making the noise when I moved into the house a month ago. If I drained the water out would that help?