The only yellow chemicals I remember is sulfur. But, I'm betting that you are seeing iron. My well has just enough iron to slightly change the taste of the water. Have it tested. I doubt that it will effect anything in your pond.
Hey, wait a minute. I guess that it could be gold. Nah!
I'm taking in samples today, How much is too much Iron? The book says avg. well water has 200ppm, I wonder at what level it can be harmful.
I like your secoond guess best!!!