I noticed last night that when I have my iPhone plugged in to charge and plugged in via the aux port on my head unit that, when the phone is paused I can hear a whining sound through the speakers that changes with engine RPM.

I know there is an explanation for this out there.

I am no expert but maybe it is because the alternator does not charge at idle or as much at lower RPMS so when you start driving the charger is putting more juice through the cable. The change in voltage may somehow be resonating through the phone into the aux cable???

Sounds like a Diesel unrelated ground loop. Check the stereo grounds or use beefier ground wire/s.

Sixto
87 300D

It's a ground loop.

Your phone is grounded at two points -- to the cigarette lighter negative terminal, through the charging cord; and to the stereo, through the signal cable. These ground points are not at quite the same voltage, so a current flows through the outer shield of the signal cable. This couples alternator whine into the signal.

The solution to ground loops is to ground everything to one point. Ideally, your stereo negative lead and the cigarette lighter negative lead should go to the same chassis ground. The other possibility would be to break the ground path between the phone and the stereo by putting a ground isolator in the signal cable, but good ground isolators aren't cheap and cheap ones will cut down on your bass.

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1981 Mercedes 300TD, 1994 Honda Civic Del Sol
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Just what sixto said. If absolutely everything else fails you can buy a ground loop isolator, but I'd recommend wiring upgrades first. I've heard complaints of sound quality loss from isolators.

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'82 300SD - Somewhere over 220k - Becoming reliable...