Koi diseases

Question
Hi Robyn!  We are new to the fish pond community and recently, we have had 2 koi die with large holes in their bodies.  One fish in the pond has that same purplish hole on his side but he seems fine.  Is that a disease, stress, food issue, water issue, or could it be from plants?  We have had a lot of moss in the pond and I have used algae killer a couple times to help control it (which it doesn't do) so could the sores or holes, be caused by the algae killer?
I'd hate to lose all the fish for lack of knowing what to do.  About the pond, it's cement, has an upper waterfall into a shallow pond (4" when not running - 8" when running), we have a large filter and skimmer that run as well as clean water input valve, and 2 aerators - one on the top and one in the deeper pond (3 1/2' deep X 6 1/2' wide) where the fish stay.

If you have any ideas, I'm more than happy to hear them.

Worried Bonnie

Answer
I'm so sorry about your koi.  Are they sores or holes?  Holes could be caused by hunting herons but I think you mean there are open sores.  Open sores on koi are often due to Aeromonas or Pseudomonas bacteria.  If that's what it is, I suggest KoiZyme, MelaFix, pond salt (0.05%), and, if possible, injected antibiotics like Baytril.  See http://www.koivet.com for more on those problems and koi health in general.  Sore areas can also be due to high heavy metal concentrations.  I suggest having your water tested for iron, copper, and maybe more.  If the heavy metals are high, you can add dechlorinator which not only binds to chlorine but also binds the heavy metals.  

I don't think plants would cause problems like you're seeing.  Food is not likely to cause large holes or sores either.  What was in the algae killer?  If it contained heavy metals, herbicides, etc., then yes, absolutely, those toxins could literally burn holes in the fish.  To remove them from the water, do a partial water change (with added dechlorinator and pond salt) and add a bag of fresh activated carbon to the filter.

Is this a new pond?  If so, was the cement acid washed?  Have you checked the pH and hardness of the water?  If the cement was not properly acid washed and cured, then the pH and hardness may be high in the pond.  The pH should be no more than 8.5.  If it's really high, that will definitely burn the fish.  Unfortunately, water changes would only go so far to fix that if that's the problem.  The pond would have to be drained and either lined or acid washed repeatedly to leach out the carbonates from the cement.

So, that gives you a few things to test and to try.  I hope things improve!