Late to this party, but sounds like a very cool project!
If you are concerned about your rock sinking into the sediment [a concern of mine, too] you could approach this a couple ways:
1. Consider using plastic or rubber tubs as spawning beds - fill them with gravel/rock mix, surround with larger boulders or cinderblocks. I have applied this method on my ponds.
2. Apply layer of landscaping fabric beneath the rock to reduce vegetation and also help prevent sinking into the muck. Bob Lusk [the Pond Boss] did this at his place.
Many men go fishing all of their lives without knowing that it is not fish they are after. ~ Henry David Thoreau