I don't know if the normal filtration methods, we use in our garden ponds, would be enough to combat this problem.
The control methods mentioned in the article, to combat the problem of iron bacteria, are not feasible, if there are fish and amphibians using the pond.
Maybe our old buddy DRH could post his thoughts on this subject? I'll try and awaken him from his hibernation!
"Horton"

I suspect the only thing that will work for this pond is aeration. It seems certain that the iron is a natural part of this environment and the problem is going to happen again and again without a fountain or two keeping enough oxygen in the water.

I think the "Prof" must be in a really deep sleep, as I note the lack of response from him. Maybe he isn't an Iron Man after all?????
More Titanium, I should think!LOL
"Horton"

So now what. Horton has pulled a very nice website that gives a description of iron water chemistry. Basically what I THINK you are dealing with is referred to as pore-water chemistry. If you had the apparatus and instruments to examine the first inch or two of the soil layer in your pond (or, for that matter, any deposits accumulated in the bottom of the pond) you’d find that they are probably anaerobic (no oxygen) after you’ve penetrated the surface just a few millimeters - say a 1/4 to ½ inch. Yep, it gets depleted that fast! In that environment, as indicated in Horton’s Wikipedia reference, iron is "solublized" and is able to diffuse to the surface. Right at the surface of this mix bacteria and oxygen increase in concentration with the result the iron is oxidized to the ferric (+3) state and subsequently precipitates. IF the iron source is in the soil lining your pond then I suspect there is very little you can do about it other than install a liner. Increasing the oxygen levels in your water will help since higher dissolved oxygen levels will cause the iron precipitation to occur deeper in the surface of the pore water/mud layer. Having increased flow through the pond will help in that it will also help promote higher concentrations of oxygen at the mud/water interface. The conventional methods for control listed for wells (typically using bleach) - probably something you’ve already come across - won’t really work with your pond since it is very likely to become rapidly repopulated with the iron bacteria. Plus it would mean cleaning everything out of the pond, etc.
The aquasphere ball that you purchased from Gardener’s Supply has nothing to do with your problem. If this is similar to what they were selling a few years ago - back then it was a plastic model - it was nothing more than a way of holding barley straw in your water. Back then you could pry it apart, refill with barley straw and re-use it! Now, of course, they’ve supposedly made it more eco-friendly by making it out of a corn-based product which ...."naturally" ..... means you can only use it once then have to buy a new one! I probably ought to drive up there and double check (their website fails to really tell you much of anything) but I’m pretty sure it is just a fancy container for barley straw.
I wish I could think of something that would be more helpful. I’d consult a book on alchemy if I thought it’d help. I even thought of having Horton run around naked in his backyard at midnight baying at the moon for three nights in a row (it’s the strongest incantation I could possibly imagine!!!) but doubt anything would really help other than what has already been discussed. But thank you for bringing a new question to the table!
—David

Thanks

Mike :)