Hello, and anyone that has any experience or suggestions, your help would be appreciated.
Just bought a beautiful '06 RX330 with low mileage. Great condition but entire floor is saturated on both sides. I started with sunroof drains.... what I immediately discovered was that where the water is supposed to drain out in the back of the fender area, is not the case. Driver's side is hardly draining... trickling out there. Passenger side the water is coming out much more in front of car.
I determined that somewhere there is blockage and the water is redirecting itself to other places. When I looked in the fender corner where I believe the water should be draining out, it is caked with mud. The fender liners have pine needles sticking out as well. I pulled a couple 1" rubber stoppers out from under the car and all the water came gushing out....
I would like to first get my new car functioning properly as far as rain water drainage, etc. I want to remove the fender liners, clean that area out and also under my rocker panels which seem to be clogged as well.
Can anyone tell me if my idea of flushing this filthy car out first is a good idea to start to find out how the floor is flooding? If so, is removing the rocker panels (or at least loosening them) to clean them out a difficult job?
I've watched a lot of videos now of DIYSers trying to solve this problem. I kind of think I should start with opening up the vehicle to it's healthy, breathable, drainable condition.

 

Rockers aren't easy to remove, would not recommend that. But definitely take the fender liner and start there and under the car. Also check the door drain holes there should be two square slits, those tend to clog/cake up too.

Also important is to get the carpets dry and sanitized, they will stink (don't ask me how I know lol).

 

Is it possible that mice put all that crap in there for nests?
I'd also double-check all around the windshield, especially the lower corners, for leaks.
Also, just for the heck of it, go in your glove box and pull out your cabin air filter. While the filter is out, check water back there, and check for leaves, mice, etc.

Other than that, maybe the door sills and kick panels can be easily removed to give access under the carpet, airing it out.

 

I just went through this last fall when I bought my 2005. Damn pine needles where everywhere. Be sure to replace the cabin filter.
Rockers are not that hard take off, the plastic cover is just screwed on but may be able to just loosen them, then blow the crap out with air or water.
Best fix for this is comment #27 in this thread. Reroute the front drains to the drain holes you pulled the stoppers out of. You'll never get it cleaned out good enough to drain reliably.
I found the rear drains are rarely an issue but you can ream out the lines with some weed trimmer line, back to front.

 

with the sunroof open, you can see the water drain holes, clean them. then i took a bottle of water and let it trickle down into the drain pipes and boom it went into the floor foot wells. there's you tube video's on it actually. take all the carpet out and the plastic molding on the right and left side of both foot well. if the holes in the cars floor are clogged then the water from the sunroof holes will come out into the foot welll. you have to then get under the car and find the drain holes and clean them out with a metal hanger wire or something similar. you'll know when the system is working properly when the water from your water bottle goes from the open sun roof holes down onto the pavement. i did it by googling, reading some posts and you tube videos

 

Hello all - and much thanks for everyone's input, ideas, and help.
This week I had my whole car gutted (by a professional, of course) and removed all seats, carpet. A real eye opener, but worth doing. The sunroof drains are clean, I cleaned out the fender liners, as best I could in the rocker panels with an air hose, the drain holes under the hood in the corners, etc. Amazing the amount of dirt, pine needles, tree droppings, etc came out.
Water tested really well and everything is bone dry. It was satisfying to do this with nothing in the car so I could really see and not just "hope".
A lot of work, but after I get everything detailed and clean carpet back in I will be proud to own this car.
Again, I appreciate those of you that offered advice.... I still have things to cover that you all suggested: cabin air filter, etc.
A side note: during this process I dealt with Lexus of Mobile (AL) even though I live in VA. They were absolutely awesome!