The rear carpet in the cargo area of the 4Runner was beyond saving thanks to the previous owner. After taking it out and putting in some new foam, I am not inclined to give Toyota $800 for a new factory replacement. Has anyone tried the Weathertech cargo liner? Does it go on top of the carpet or replace it?

The Weathertech cargo liner goes on top of the existing carpet. it is nice but the lip edge to contain water at the rear end can get in the way during loading (at least that was true with the one in my dad's van and the one in for the 1st gen Sequoia.) It is hard to tell if this lip exists on the one for the 4thgen 4runner cause the images show the models for various cars and some have them and others don't. On the Van we just cut off this 2" lip with a razor knife cause it was always in the way loading and unloading. IIRC it's still there on the Sequoia but kinda folded over.

There is also an OEM carpet mat from Toyota that I used on top of the OEM carpet to protect it before I put in my drawer system. It worked well and would hide most sins on the floor area similar to the Weathertech.
You might look for Toyota Part No.: PT548-89031-11, PT548-89040-14, or PT548-89032-11 These are the ones that I have for my 06 as these are generally available for ~$50. The part numbers depend on if you have the tray installed or not and color of your interior. They have more for rigs with the 3rd row but I don't have the #'s for those.

Boort

Boort

I have one in my 4th gen. It's been in for the past few years since I bought it. I have used it while camping or sleeping in the truck and for moving things. In my opinion, the lip is flexible and doesn't prevent you from loading stuff. If does work well to prevent water from going onto the nearby carpet.

If I had one complaint, using the cargo net with the liner does cause the liner to lift in the corners due to the bungee cords which connect to the loops which are unfortunately covered by the liner. My fix for this is to disconnect the net from the side connection points while the net is not needed.