the holes are probably muskrats. I have caught three of them at my pond this year already. Search "muskrats" to see lots of threads about what they do to a pond and how to catch them.

I am no expert on the stuff in the pond. It would help to have a close up of some of it. Maybe you could scoop some out and get a picture. The pros will be by soon and give you all the info you need.

Brian
Retired Coach

Just another day in paradise!