Bed Rust, What to do?

The sheet metal isn't very thick. It's about 1/32. The floor itself is a bit thicker, at 1/16

I agree it is not severe rust, as it didn't rust through, but this spot is a very unconvenient place when it comes to treating rust because it's right on the seam. If you want to treat it, use a rust killer/converter and make sure that it goes into the seam as well, not just on this spot. Then put some primer then a few layers of paint then apply the bedliner.

The big problem is the bedliner itself. If rust ever comes back, it will trap the rust underneath, but try to treat that now that you have rock-hard bedliner over it :/

if you want to be sure of getting rid of this rust, cut it and weld a patch

 

Phosphoric acid, such as Ospho. Converts rust to iron phosphate, killing the oxidation reaction.

Of course, the only way to be sure is what was mentioned: cut it out and start fresh.

 

I really appreciate the responses. I have already sprayed Permatex rust treatment 3 times and blew the Permatex between the two pieces of metal with compressed air. I may cut the top layer(side) off and then brush the bottom layer(floor) down to bare metal. If the floor cleans up good, then weld in a piece of appropriate sheet metal before top coating.
Here's a pic after Permatex rust treatment.

 

Anyone ever painted the underside of the bed? Mines showing a lot of rust and I was thinking about using some POR15 metal prep and Por15 paint i have left over from my recent frame painting

 

Are you thinking about removing the bed to do this?

I had the typical rust spot near one of the wheel wells. Here's what I did.
https://www.tacomaworld.com/threads/removed-the-cancer.563010/

 

Yeah i have access to a big gantry crane and was going to just lift the bed up and coat the underside with por15 and a quick topcoat. Im not at the point of rust holes but have signigicant rust along the cross bars/supports and the wheel wells.

 

I just finished this type repair. Same cause, plastic bedliner. I didn't use any body filler yet on the inside of the bed, but I used to commercial rubber roofing material to seal the patch on the underside. It's a little close to the heat shield, so we shall see if it gets hot and comes loose...

I am only putting a rubber mat back in bed, so I may use some body filler to pretty it up a bit. But maybe not. It is a 25yr old truck after all . I did spray w/gray paint since pic. Looks okay.