Went for the car's (2010 IS250 C) annual inspection, and mechanic found that the bottom portion of the trunk was full of water. Took the car to a Lexus dealership and they found that one of the drain holes on the upper left side of trunk was completely clogged. They sent compressed air and this fixed that problem. Recommended that I send forced air in both drains about twice a year to make sure they don't clog up again. After washing the car back home, I noticed that there was still a little water accumulating in the bottom part of trunk again, but much less than last time. I gave the trunk a personal verification, and this time found that a small portion of the upper seal around trunk had let go. Now taking car to dealership to have this fixed. Have owned many cars in the past, and this is first time this has happened. Car is stored during winter and has only 20,000 mi.

 

I had the same problem a few years ago when i didnt have a garage, upper seal on the passenger side ripped or something. Water filled up the lower portion of the trunk and my compressor sucked up water and failed. Had the dealership fix the the weather strip and all is good now. Now the car is garage kept

 

Finally solved problem, well there were 2 problems. The first time was that the water drain on drivers side of trunk was clogged, so air pressure was used to clear it. Did water test again and water was still seeping in, however much less then previously. Further check revealed that a small portion of the trunk seal on the drivers side had let go, so dealer agreed to replace it. Hopefully this will fix problem once and for all.