This is a good one for Bill Cody. Part of his service is to identify microorganisms in water. From a sample of your water, he can tell what types of critters make a living in your wet stuff. And, he can also tell you if the coloration comes from dissolved minerals. Contact Bill via his e-mail address from one of his many knowledgeable posts on this site.

Teach a man to grow fish...
He can teach to catch fish...