I don't think you will have any problems as any gases that are exposed, if any, should just off-gas into the air.

I've done this same backhoe type thing in my pond to create some deep holes and it's worked fine.

Excerpt from Robert Crais' "The Monkey's Raincoat:"
"She took another microscopic bite of her sandwich, then pushed it away. Maybe she absorbed nutrients from her surroundings."