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I would see a foot plus of ANY substrate as very likely to go anaerobic. I would not add that much.
6" is probably fine, and you can get the plants to root in that much, and the plants will keep it from going anaerobic as long as they are growing well. In the winter, however, most plants will go dormant, and this means little or no oxygen exchange aided by the plants. Just whatever the water movement does.

Water lilies are big plants and would really like the depth of this pond, too. Another reason for not filling it in.

However, if you really want a shallower pond I would remove the liner and fill under the liner, then replace it. That way you would have a shallower pond without that enormous mass of soil to go bad.

Planting in containers is a very good idea, to be able to remove and prune as needed, but planting directly in the substrate will allow the plants to bring oxygen down into the soil.

Substrates mix over time. I would not bother setting up a layered substrate.

How to walk in a pond that is 4' deep: build a walkway out of rock (difficult, but no chemical issues) or CMU (VERY easy, and you have all winter to get rid of the GH and KH that concrete products will introduce). Buy a wetsuit (or even a dry suit for those really cold days). Tiny boat? Maybe I am getting silly! :rolleyes:

Drainage, filtration, and water movement: In my smaller pond (only about 250 gallons, and a hill-and-stream style) I found the substrate would go anaerobic with less than 2x the pond volume per hour of turnover. I actually ended up with over 1000 gph because I like the sound of the waterfalls.
Here is one possibility to keep the water moving through the substrate: Set up the intake using a manifold of drain pipe with LOTS of holes in it, and covered with filter cloth. This would be built in the pond so that the pipes are no farther apart than 3', and closer is better (such as a 2' spacing). Then use a pump that will give you something close to 2x your pond volume per hour. The water being pulled through the substrate will keep it aerated.
 

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