Cat, I think you're really on to something. If you pump from the main pond I've always heard that the best quality water comes from the middle third of the water column. Too far down to have tons of algae, and too far up to have tons of organic waste. Take my word for it--ponds like this can be fish producing machines if you can bring in all fresh water a couple of times each day. It also seems like your little ponds are about the right size.
