My guess is that you are talking about the rear speakers. This is a somewhat common problem and it has happened to me before.
Take a look at the rear left and right windows. The corner pointing towards the rear of the car probably has a small gap. This gap is not between the window glass and moulding but between the moulding and the body. Water enters this gap and leaks down through the inside of the car. The windows need to be resealed.
Another possible cause if you don't have the window gap is the sunroof drain tubes getting plugged. There are four drain tubes, each on one corner of the sunroof. The front tubes run through the A-Pillar and are not relevant to your problem. The rear tubes run through the C-Pillar, they are in close proximity to the rear speakers. These tubes would need to be cleaned out.
The car I had this problem on was a '97 GS automatic that I bought for $1100. I couldn't be bothered to fix a small (for me) water leak that happened sometimes when it rained really hard.
