There's an 89' Trans Am that I'm going to look at this week, and it has holes in these two spots, which are in the rear wheels wells infront of the wheels. I had them repaired on my last GTA, but I can't remember what this area actually is. I know it's a super common spot to have rust in, but is it part of the car's integrity at all?

 

If you mean the tiny holes near the bottom of the inner wheel well, it's not exactly structural. The inner wheel well is basically a skirt to keep debris away from the rest of the car. At the bottom edge it's open on both sides up a couple inches from the bottom, then you'll have a flange where the panel behind is welded. Easy cut put and weld in patch, as easy as a thirdgen gets anyway...

Bigger question is how much more rust is there that you can't see from the top?

 

Apparently the floors need a few patches but I haven’t seen it in person yet. Just wanted to make sure that it’s even worth the drive with the spots in the pics. Body looks beautiful and if the rust isn’t too bad, the car’s a smokin’ deal.

 

Check up front around the tabs where the fenders bolt to the rocker flange. If you've got rust in back, it's a safe bet the bottom of the A-pillars on both sides, and the rocker flanges are probably compromised.
Look around the strut towers, and the rear corners of the engine compartment where the wheel wells meet the firewall. Check out the battery tray. Usually you'll get rust in those areas from sitting out in the elements since the run off pathways where water tends to collect and drip out, will get filled with leaf debris and dirt. Eventually the water can't run off and you get a hole. If the rocker area rusts out, that debris and water will run into the rockers and rot the rockers out. Rust in the rear wheel wells above the tires is fairly common too. The rear spring and shock mounts aren't far from the rear wheel wells. Rust in suspension areas and frame rails is what I would consider fatal. Rust in the floor pan that doesn't get into the rails can be fixed, a person just has to decide how bad they want to mess with it. A "rust free" car is usually the same price and saves a lot of really dirty tedious work.

My project's shell had rust in the rocker flange on the driver's side. It extended from the fender mounting flange up about 6" into the A-pillar. Couldn't see it until the fender was off or the carpet and wiring was pulled back. It still didn't look that bad, but the piece that rotted away was sandwiched between 3 other layers of steel, as the panels were all layered together and spot welded as a stack. It took a bit of creative spot weld cutting, and peeling back layers to get to the bad piece. Then I had to reform everything I'd peeled away or cut away, and weld it all back together. It turned out OK, but I probably would have passed on the car if I'd seen the rust before buying. I wouldn't voluntarily jump right in and do another one.

 

What Drew said is 100% right on. I just went through repairing all of these areas on my GTA and would never do it again given that there are so many rust free cars still available. I started off with just fixing the "only" rusty area and then I found another hidden area and another and so on until I had the car torn down to a completely bare shell.

That lower quarter panel rust behind the ground effects is a very common spot and if its bad enough to have spread out of behind the ground effects, its pretty much guaranteed that the other locations Drew mentioned are all compromised too.

Go ahead and look at it, but be ready to walk away.

 

Thanks for the input fellas. I kinda figured already that with holes like those, there's only more to be found. I may still go take a look but the car's an hour and a half away, so we'll see