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I've been chasing this leak for months now and can't figure it out. Anytime the car gets wet, water collects in the back seat, mostly the passenger side, but sometimes the driver as well. It was diagnosed as needing a new roof (and the car was nearly 20 years old with the original), so I had it done. Water is still getting in though and my father and I think maybe we found it. Water seems to be coming in where the roof meets with the rear frame or windows and runs down to the back seat. The shop that did the roof was terrible, so there could have been multiple points of entry that have been eliminated down to this or this could have been the problem all along and they lied to me. Who has experience with this and can advise what to do to keep the water aimed for the drain tubes and not my backseat?

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Did the leak happen before or after the top was replaced?
As someone inside watches to see where water is coming in use a hose to douse the roof above where the water is entering.
 

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I have a 2001 GT Convertible which had water seepage that would would pool in the area behind the rear seats and could also end up on the rear floor well. I first knew something was wrong when I drove the car in horrendous storm and had the car sit outside for a few hours . I never drove the car in the rain before for several months after i bought it used in 2008. I would hear sloshing water when making a sharp turn and did a WTF. Most shops wanted to replace the entire top but I found one place that knew exactly what the problem was . He told me that there is a design flaw with the rear window section of the top that channels water and it flows into the interior . The fix is a new rear window section that has been rengineered to avoid this. After the new section was done I went through a few weeks of torrential down pours in SFLA and never had a leak since then . I did have new hydraulics replaced with top quality replacements and some wiring replaced as they found oil leakage once they took things apart. Total bill was under 1 K several years ago and I have never had an issue since then. It was a great experience with a business that knows their business and takes pride with their work and knows how special the vehicle is to their clients.
 

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2004 GT convertable 40th anniversary automatic
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I have a 2001 GT Convertible which had water seepage that would would pool in the area behind the rear seats and could also end up on the rear floor well. I first knew something was wrong when I drove the car in horrendous storm and had the car sit outside for a few hours . I never drove the car in the rain before for several months after i bought it used in 2008. I would hear sloshing water when making a sharp turn and did a WTF. Most shops wanted to replace the entire top but I found one place that knew exactly what the problem was . He told me that there is a design flaw with the rear window section of the top that channels water and it flows into the interior . The fix is a new rear window section that has been rengineered to avoid this. After the new section was done I went through a few weeks of torrential down pours in SFLA and never had a leak since then . I did have new hydraulics replaced with top quality replacements and some wiring replaced as they found oil leakage once they took things apart. Total bill was under 1 K several years ago and I have never had an issue since then. It was a great experience with a business that knows their business and takes pride with their work and knows how special the vehicle is to their clients.
This is the answer I have been looking for. My top also leaks around the rear window and collects in the boot area behind the back seat. Thanks for the info!

Thanks for the info. I've been chasing the same leak that pools in the boot area behind the back seat for a while now. Rear window replacement sounds like the answer.
 

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2007 Mustang GT Convertible
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Check your weather strips for the windows are forming a decent seal, also make sure your short drop function for the windows is forming a tight seal into the roof, you will also see in the bottom corners of your doors have little rubber water drainage bungs, remove them and make sure there isn’t debris build up in the bottom of the doors preventing water draining from them
 
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