The holes are holes in the ice, so I guess they're ice holes ;^)
As for what caused them, I cannot say with certainty. I only imagine there is some sort of warm upwelling that keeps the ice from forming easily. I saw them in different areas; some shallow and some deep water.
I used Topaz Labs' Black and White Effects. I am a big fan of Topaz's plugins!
Sorry it took so long to respond.