I started to see tiny rust spots popping up on the roof. Gobi Stealth rack. Took the rack off and found rust building up in the water drains as well. Not terrible yet. I am in Panhandle Florida near the coast and definitely have not washed my vehicle as often as I should. Also seeing rust on parts of the rack where the powder coat is chipped off.
Getting the roof repainted and will get a clear film or color match wrap on the roof for when I put the rack back on. Haven’t looked at the mounting points yet, still have the rack mounts in to prevent water damage until I get some OEM hardware. Definitely going to use the Butyl silicone.

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First, my condolences to OP. This sucks pretty bad no matter how you look at it. However, I do believe it's repairable, but at what expense? Personally I would take it to a body shop and see what they say. They probably replace roofs all the time after hail storms. Estimates are free.

Also the root cause may not matter so much to OP, at this time, because the damage is done. The root cause is valuable to others that may see the same issue.

For the the non believers in galvanic corrosion, it's real. In this article, he states
Note that he say's zinc galvanized on a steel beam. Or in our case a zinc screw and steel body.

The OEM rack has a rubber piece under it called "End Support Insulator - Toyota (63487-35020)". They also isolate the aluminum frame from the body by using a support plastic bracket. Finally the hardware looks chrome not zinc plated.

We had our Frontrunner installed for less than a year and needed to pull it off. The Frontrunner (steel) spacers had started to rust pretty bad and was contacting the roof. I contacted Frontrunner about it with pictures and heard nothing back. Fast forward a few months and I see they now come with plastic spacer blocks instead of steel. In their defense, they sent me a set of plastic ones instead that we plan to install after removing the rack and taking care of any surface rust issues (if any are present).

In the world of mods 5th gen mods, the roof rack has been our most frustrating but is actually one of our most used. It ain't up there just for looks, but there's no free lunch.

Yes, galvanic corrosion is a real thing. No, it is not the primary reason this happened (root cause).

Galvanic corrosion can only take place in the presence of an electrolyte (in this case, stagnant rainwater and moisture). If the roof holes and hardware had been sealed correctly, it would not have corroded, galvanic or otherwise.

Yikes, that sucks. Hopefully it works out for you. I knew that the Ecotechne roof had a ton of complaints about its powdercoat finish and hardware, so I took a lot of time when I prepped my rack install. So far I haven't bothered with it in the last 1½ years, but will keep an eye on it.

I should clarify: we needed to pull it off for other reasons, not due to rust issues. We discovered the rust issues because we removed it. Glad we did. I’ve saved the butyl sealant thread for future use!

Yes, that is correct. He was stationed in Hawaii and San Diego, both areas have lots of salty moist air from the ocean. I think that would qualify as an electrolyte.

It can, but there shouldn't be any bare steel exposed to the outside air on a correctly installed roof rack. Plenty of people drive 4Runners in Hawaii and San Diego, and their roofs don't look like this.

Not trying to hijack this thread, but think this is relevant.

I posted recently on the forum about my 2018 that I got a few months ago. It came with the kit to blank out the roof (i.e., no roof rack). I decided I wanted a stock roof rack and found one cheap locally. I installed it, not disturbing any of the rubber slats that fit in the roof channels. After a recent rain, I had water on driver's side floorboard. I narrowed it down to two holes, one on each side of the roof (unplugged about 12 inches back from windshield.) under the rubber strips. I also found a fair amount of surface rust under those rubber strips, only in the front, as they were being held down with double-sided tape...not my job. I've fixed the rust and plugged the holes and no leaks now, but I'm wondering if I should put the strips back on...they're really cosmetic. Others have glued them down...debating that, maybe just the front strips? Anyway, thanks for reading...sorry OP for damage to your rig. I don't feel like there should be rust there for a two year old 4Runner that came from Arizona...?

I have the Sherpa Crestone on order right now. Should be coming in about 3 weeks. After seeing this thread, I sure hope their rubber spacer will be enough to keep the water out.

Ok, if there are holes 12" from the windshield, it's very possible that an aftermarket rack was installed before you received the vehicle. Those holes are not there from the factory. Many aftermarket full-length racks require extra holes and mounting points, instead of just using the 8 factory holes that are at the middle and rear of the roof.

If you received the truck with a rack delete kit, it sounds like they removed the aftermarket rack before selling it. These are threaded and sealed factory pieces, so those should be fine- along with your new factory rack, as long as all of the correct seals and hardware were also installed.

However, those drilled holes up front should have been sealed more adequately. I assume the holes have rivnuts installed, and they should have had thread sealant and set screws to fill the holes. The rubber strips along the channel are not seals, they are merely pieces of trim that fill in the roof/body weld seam. Whoever the previous owner was, they did not do their due diligence when removing their aftermarket rack.

Whoever you bought it from (dealer or private party) you should strongly consider returning the truck for your money back, or insisting on them paying for a detailed interior inspection and refurbishment. Not only is your carpeting and trim prone to molding, there are also sensitive electronics and wiring in the footwells that are sensitive to moisture. Many people have had to replace large amounts of wire harnessing and electronics because of corrosion in this area. Press the issue! Your truck may be severely compromised and prone to faulting out because of this installation.

That doesn't look too bad. Before getting the roof repainted I would try to clay bar the roof and entire car while you're at it. A lot of times you can get rid of those small round rust rings and spots with a clay bar. Then give it a good wash along with a coat of wax or ceramic coating. I think if my clear starts to erode from sun exposure I'll probably wrap it in matte black. However it's still crucial in sunny states to wash and apply wax or ceramic frequently.

Okay.

I did the cleaning beforehand. I was good with it until I opened the sunroof. It was really bad. Took it in and they had it fixed in a couple days. I think my issue has to do more with my wind deflector, the rubber was rotted when I took the rack off. Luckily the 3M strip held up just long enough. Definitely have to stop being lazy when I clean the car and get on the roof.

You don't sound convinced. Okay, let's review. For galvanic corrosion to occur, it requires dissimilar metals to be touching each other in the presence of an electrolyte. The metals can be expressed in terms of being "noble" (ability to resist corrosion) and "non-noble" (tendency to corrode). This is called galvanic potential, and it can be expressed in terms of voltage differential across the two metals in the presence of an electrolyte. Take a look at the chart near the end of this page (anodic index): Galvanic series

Looking at the relationship between plated/chromium (stainless) steel and plain carbon steels, the voltage differential can vary between 0.15V to 0.30V, which places it in the "acceptable outdoors" to "monitor/caution" range, depending on exact alloys used and conditions present.

For example, on my roof rack, I've used 316 and 304 stainless hardware to assemble it- this actually places the voltage differential (and therefore galvanic potential) higher, in favor of the hardware. Using your example of salty sea air as an electrolyte (I also live near the ocean as well as visit mountains during ski season), that means that my roof should be corroding to pieces around the more noble hardware.

However, that isn't true- see the picture below for a picture I took today, with the hardware and roof looking the same as the day it was installed. The reason for this is because the metals are isolated from one another as much as possible (the sheetmetal on the truck is painted, the rack is powdercoated, the threads where metals might touch have thread sealant applied, etc.).



I have also made sure to seal the interface using weather-resistant rubber washers and butyl rubber sealant, which allows any water (electrolyte) to drain and evaporate away from the area as quickly as possible, in the same way that the factory roof rack does. This ensures that even with a galvanic potential present, it's isolated from the electrolyte (water).

This is important, because using silicone/UTV sealant (and especially when it's poorly applied or applied several times) may not provide the dynamic seal needed for heavy use outdoor applications. Moisture creeps in to the small crevices that are not sealed, and stagnates in the threaded holes in the sheetmetal. You don't need dissimilar metals to begin oxidation in this case- steel will rust on its own accord. Using your logic, I should have selected hardware with less galvanic potential, like plain uncoated steel. But that would simply accelerate normal oxidation and the hardware would rust due to exposure to the elements.

To sum up: yes, galvanic corrosion is real and must be accounted for in certain applications. However, isolating metals and preventing moisture buildup is even more important. If you understand and apply practical methodology when installing a roof rack, you will be fine- the same way Toyota is fine when they install the factory roof rack. Toyota builds and sells thousands of 4Runners every year, and very few have Swiss cheese roofs. If you poorly seal the roof rack mounting locations, no amount of galvanic similarity will save you.

Looks clean. Where is the butyl rubber sealant applied? Looks like the bolts are on the rubber washers. Is it below the foot?