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Recently I heard a sound coming from the water heater DURING USE,
perhaps from near the top. It's not as violent as a knock may sound,
but I don't know how to tell the difference between a knock and a
click! So it's one of the two. The sound does not seem to happen after
use, only during.

As you drain out the hot water, cold water is replacing it. You can get
some noise from the expansion/contraction that takes place as well as the
two waters mixing.