If you find water pooling in the rear passenger floor, especially the driver side there is a quick way to see if the problem is coming from the front drivers door. The front drivers door is the unlikely source of many water entries and it is easy to check, yet often gets overlooked because the Bonny does a great job of hiding the "underground/ undercarpet river".
Have water collecting here:
Then remove this plastic strip, pull up the carpet and look for water in the unibody channel. If the water has been leaking for months, the door speaker may also provide a sign as this door speaker has signs of water and the other three door speakers do not.
I was not able to place the photos in sequence, but these crude pics may help some discover the water problem. Anytime you discover water in your Bonny interior and the sunroof is not the issue, the next question you may want to ask yourself is- has the interior skin of the door been removed. If the answer is yes, a high probability when the skin was removed, the door was not resealed. GM designed these cars to have outside water flow through the inside of the door and back to the outside. I can't imagine why- but this is how it works.
2001 Bonneville SSEi, 219,000 miles.
Whats in my driveway:
1998 Chevy S10 4x4 ZR2, 1999 Olds Bravada, 2001 Pontiac Bonneville SSEi, 2007 Ford F-350 regular cab 2WD, 2008 BMW 335i coupe (Wife'* replacement for her Bonneville). The Bonneville is my favorite of all the cars in the driveway.