What I would do is buy a small pump and have it hooked up to a hose.
Lay it on the empty pond bottom and have the disharge hose feet a long
ways from your pond so the sudsy water would never drain back toward
your pond in a heavy rain. Then I would take a garden hose and start
spraying the entire pond. Once I got about 50 gallons of water in the
pond bottom I would start the drain pump and get rid of the water. I
would repeat this process until I saw that there was no sudsy water.
Then I would do it a couple of more times just to be safe.

After that initial cleanup I would get a large mesh bag and fill it
with Zeolite or Activated Charcoal and then put a couple of rocks in
the bag and sit it into the waterfalls filter. Then I would fill the
pond and run it for a few days. I would then dump the Zeolite/Charcoal
and drain the pond completely one last time. Fill the pond back up and
add another bag of new Zeolite/Charcoal and then let the pond operate
normally.

Paul
www.pondkoi.com