The sliding rear window is leaking on my 07. I must be coming in and runnig down the back wall because the storage under the rear seat is filling with water. I have run silicone all the way around the outside of the back glass and sealed the 3rd brake light. Any suggestions?

 

Have someone stand in the bed with a hose and spray it down while you are in the back seat looking for the leak.

The 3rd brake light is usually the culprit, tho...

 

Agreed, third brake light. Remove it, clean off the old gasket, and seal it back in with clear silicone. Only a Phillips screwdriver is needed. Takes about three minutes. Problem solved.

 

On my 06, it wasn't the 3rd brake light that leaked, it was the seal at the top of the back glass. I bought "flowable" window sealer from an auto parts house, O'Reilly's I think it was. Using a short piece of drinking straw taped to the nozzle, I was able to get the sealer into the small space between the top of the window and the cab. Leak stopped!

The key is to use the flowable sealer, rather than regular silicone. Good luck!

 

On my '07 I had the exact same problem, turned out the rubber seal on the window that slides wasn't sealing. I ran a line of vaseline between the sliding window and the rubber seal. Fixed the problem, unfortunately I can't open the slider, unless I want to break the vaseline seal.