I would like to set the stones permanently on the bottom so we could really brush on and around the rock for a thorough cleaning, rather than remove, move and get under the rock, which has never gotten the thing clean.

I've tried getting advice from a tile/masonry forum, to no avail. And, in my research, I have come across black foams, hydraulic cements, regular mortar, plastic cements. My eyes are now crossing. Basically, I would like some advice on a good product to trowel across the bottom and push the stones into, so they stick out of the cementious "bed" and look like rocks, but stay in place during cleaning. It would have to be a product that stands up in a submerged environment.

In terms of toxicity, the hope would be to have at least some pond plants in submersed baskets, but fish probably need a little more depth than I have.

Thank you in advance for any thoughts.

I'd leave them be unsecured. You can move things around, and really get in there and clean if needed. Once you glue stuff down, it just makes it harder.

Just my $.02.

If you must secure them, black foam would probably be best. It's for underwater environments and should last. I'd be leary of any type of caulking.

I like the look and cleaning is easy, no muck build up.

Have you noticed much shrinkage around the rocks? Mine are 2-3" in diameter so that might be an issue.

This is time consuming. You might consider using the methods they use to produce exposed aggregate. Even stamped concrete. 30 sq ft isn't too bad. But for me I used larger and larger rocks the more I did, using large flag stone eventually. Depends on the look you want.

I did use small 3" river rock in some areas to vary the look. It didn't turn out that well for me, kind of just looked like concrete. Unless you you're going to use chlorine to remove all algae the small rocks get a little hidden.

Thought about using broken slate? Cleans really well and you can get a modern look if algae is controlled. Pretty inexpensive too, faster to lay.