How can I clean these brown iron stains in my pot?
If it's rust stains or other kinds of scale build up, CLR will take care of it: 

http://www.jelmar.com/CLRbasic.htm

From the pictures (thanks for adding) it looks like sediment from the water (source, pipes, etc) and CLR cleans it easily.  Just don't breath the fumes.

Also, you can try commercial coffee pot cleaners such as http://www.urnex.com/ to remove the build up. 

Finally, if none of the above is available in your area, try Vinegar first.  If that didn't work, wash off and switch to baking soda.  you may have to make a paste and let it treat for a while.

There is also this recipe for cleaning rust stains from aluminum pots, though I haven't tried it.