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I have a 2009 E350 that I've owned for 4 months. While nosing around the trunk shortly after purchase I found the trunk fuse panel and HK amplifier behind the driver's side trunk trim. I also found a discolored wadded up paper towel sitting on top of the amp that had what I now suspect were water stains on the towel.
Recently, after driving in heavy rain and through 4-6" deep standing water, the rear deck subwoofer (and maybe speakers) began popping and crackling, even with the audio completely OFF. After searching the forums here and elsewhere, I pulled apart the trunk and found water around and in the spare tire well along with evidence of past water intrusion and the insulation below the amp was also very damp. I think that explains the wadded up paper towel I found in the trunk amp/fuse compartment. Part of my trunk trim on the driver's side is deteriorated (pics attached) just beyond where the trunk lid curves from horizontal to vertical when closed (the trim in on the closed vertical portion). It is possible I'm getting water in there and I also looked at the amp vents that exhaust into the wheel well to see if any were blocked and perhaps I was getting water in there, especially after driving through deep standing water like I did recently, but the vents appear to be in good working order.
After drying out for a few hours, the sound went back to normal and remained that way even while driving in rain until this morning when I drove in some rain (nothing super heavy) and I again had the same popping, but this time it stopped quickly but then a hum began. The rear deck (behind the rear seats) speaker(s) had a constant humming sound, varying in pitch with acceleration and deceleration of the car, even with the audio again completely OFF. I turned off the Logic 7 surround with no effect, moved the fade full forward with no effect, and had good sound from the speaker when moving fade full aft even though the hum was still present. I made a recording of the sound but cannot attach it since it is an m4a file from my iphone. I turned the car off and the noise stopped so I then inspected the trunk but didn't see any water, the insulation below the amp was dry, and there was no water that I could feel on the subwoofer when accessing it from the trunk. When I had the trunk apart a couple of weeks ago for the initial problem, I saw a number of wires on what I think is a common ground point on the driver's side trunk wall outboard of the fuse box. and they appeared secure.
If anyone has an idea for a quick fix for this issue I'd sure appreciate the help.