"The well was depleted of water."- OK
"The overuse depleted the well of water." - I'd remove 'The' before 'overuse'
"Water is not available due to the depletion of the well."- This sounds stilted to me.
"The well is useless because of the depletion of water." OK
It also depends on the formality of the context- normally I'd say that the well dried up, or maybe use extract/overextract
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