Because your planned gravel spawning areas are relatively small, consider first putting down landscape fabric or weed block material under the gravel. This can help keep the gravel from working its way over time into the clay bottom, and 2. It should allow you to use a littler thinner layer of gravel in the spawning beds because the gravel will tend to not blend into the clay bottom.

Another thing I would do is outline at least one outer perimeter of the bed as a test area with cement blocks or similar retention border to keep the gravel edges from blending or moving into areas of the outer adjacent sediment. Over time expect the gravel areas of each spawning area to become infused with organic sediment. It is how aquatic nature works. An annual raking of these gravel areas helps keep the organic better decayed and cleaner. Nest building activities of fish also help keep subsurface spawning areas in better oxygenated condition with less organic buildup.