The strange rust colored water may be due to things falling in pond, I have had my ponds for over 22 years now in the same place, and every year like clockwork, the water starts to darken into a pretty golden color. It can get quite dark and then the pond bottom cannot be seen for a short time, maybe a couple weeks or even up to a month! Twenty years ago I too used to wonder how this would happen, fish seemed fine, water was darkened but very clear. Then I noticed that the bowls of water that I would set outside for the dogs would darken too, to the same deep golden (almost rusty) color. I finally figured it out, it was very small black pellets that fell everywhere like sand falling from all the trees. It was Caterpiller dung!! A very potent fertilizer for the yard and the pond! When the caterpillers come, the pond plants really start to grow good, and the caterpillers eat the finest greenest youngest leaves, so their dung is a very dense form of peat extract almost. I used to pay good money for concentrated liquid pond peat, but the caterpiller dung does the same thing!!
Watch and study your surroundings and look for clues as to what may be causing this in your pond. If you have lots of trees, it is probally the same thing, or something very similar. Not to worry, the caterpiller don't stay for too long, they transform into a moth or something. The caterpillers are a good thing, if it were not for the caterpillers the trees would take over my yard!!
