I'm getting the leaking rear windows on my TJ Wagon repaired today.

However, since i unknowingly had some water in the wheel well the last month I have some surface rust now appearing.

What's the best way to get rid of this?

Do i use a wire brush then give it some anti rust paint?

I wasn't really keen on changing the colour of the wheel well, making it obvious in the future that rust was there, but is it the only option now that a bit of rust is appearing?

Thanks.

Wire brush, coat of anti-rust paint is the way to go. If you are thinking of prospective future buyers, best be honest and explain why if they notice. Some buyers will be more interested in what you did to fix the leak, while others (expecting a second hand car to be pristine with no problems or history of problems) will shake their heads and go away.

If you have had a puddle of water in there for a while, chances are the spare is rusty in its steel belts. Expect it to creak a lot if you ever use it. lol

hi walkesh. i too am having trouble with water entering the wheel well. I am looking at replacing the seals in the two fixed windows and the hatch window of my wagon. Can u tell me where you got your window seals replaced at, and what was the cost.
Thanks

Ring up any windscreen replacer and ask for a quote. Worth it, whatever the cost!

The right way to treat rust its to wire brush/sand/scrape and rust off of the surface hit it with a coat of rust - prime (Septone)/converter(Motospray)/eater(Wattyl Killrust) (all same thing just different name), 2 coats may be needed it its heavy rust, then apply a Zinc Rich Metal Primer, this will prevent rust from returning, then a topcoat of enamel and all is complete.

Higgybooboo, I used Ace Windscreens. He's a mobile repairer that works out of the Blacktown area.

http://acewindscreens.com.au/

If you aren't in Western Sydney, just google windscreen, autoglass etc.