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Discussion Starter #1
Source #1: Underside of rear carpet wet. Seal of vertical seam in back wall below corner of back window cracked open. Water from roof gutter drains into rear window gutter then flows right down this seam. Leak soaks carpet around lower rear seat belt anchor bolt, runs down under rear foot well carpet and drains into rear rocker panel gutter. Fixed by pushing silicone into hairline joint by rubbing sealant-loaded finger across the edge of the seam. Finish up detailing joint with small art trowel.

Source #2: Underside of front carpet wet. Positioning peg on back inboard seat anchoring bracket missing its thick soft rubber gasket. Undercarriage splash water gets in around the peg, seeps forward under seat into driver footwell, then outboard to front rocker panel gutter. Carpet backing has foam blocks that sit in the gutter marinating, never dries out. Fixed by installing 1/4" thick squishy rubber washer on peg, silicone around hole before dropping seat into position. An old neoprene mouse pad is good material for this gasket.
 

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I have the same problem. Pictures would help a lot, I have my 4 channel amp along with my subs and sub amp under the back seat. Water and electronics don't mix.
 

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Discussion Starter #4 (Edited)
I didn't take a lot of pics when the back wall and side wall trim were pulled off. Too busy trying to solve the problem. So no photos of the rear leak area on the inside. Doesn't matter - you can't fix it from the interior anyway.

I can offer these:

Arrow on offending seat position peg hole causing leak that runs lateral and forward into the front footwell. You can see the water staining around the hole (which has some rust stain) and running down into the front footwell. It eventually makes its way to the forward rocker panel gutter.

Arrow on offending exterior joint causing leak that runs down rear wall corner with side wall, wetting back carpet near seat belt floor bolt, then running further down and laterally into rocker panel gutter. This is the repaired joint with silicone sealant.

Same exterior joint on passenger side. The OEM sealant is starting to crack here too. I need to attend to that. Not leaking yet.

Forward rocker panel gutter near threaded hole for forward outboard seat anchor. This is forward of divide between front and rear gutter (not shown). I believe that thing is the side air bag trigger, so handle with care.

Arrow on seat peg and homemade squishy gasket with seat reinstalled. When the seat is in place, the top of the peg has at least 3/16" clearance from the floor, so gasket needs to be on the order of 1/4" - 5/16" thick, very soft and closed cell waterproof. The Spenco insole material I used is probably not closed cell, so I coated the bottom with silicone and put silicone around the hole before putting the gasket on the peg and dropping the seat peg into the hole. Tried to keep silicone out of the hole in the gasket and off the peg so the gasket will stay glued to the floor and not get ripped when / if the seat is removed again. The red rope is threaded through the channels of the seat bracket to provide a tie-off for king cab cargo.
 

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Hello, I discovered the same issue, water is getting in via the seam in the rear pax side. My truck is black, what type of sealant should I get to fix this issue as you described in your Source #1 leak?
 
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