Recently added some Water Lilies, not doing as well as expected. Not sure what to make of this.
Planted the tubers in large pots 3 feet deep, they had a few leaves, a couple inches long at the time. A week later, leaves to the surface and more on the way, up to seven leaves each plant! The leaves are red in color when growing and at the surface, but they didn't last a couple weeks before turning brown and disintegrating away. Now leaves keep coming but, they seem to die shortly after reaching the surface.
The Lilies were removed from a small Lillie overcrowded backyard pond nearby. I looked at the pond they came from, clean healthy water, beautiful red flowers. The owner did not want to throw them away, so held them in a plastic container, and put them in the classifieds for free, not sure how long they were in the container.
I'm new to lilies this year, but I would try to place one of them in shallower water and see if it reacts positively to it. Some of my smaller specimens do not like to be in water much deeper than a foot. They would throw a leaf or two to the surface and then they would get slimy looking and rot off the stem. I moved them up from 18 to about 8 and they are doing better. My plants are hanging from baskets off the dock so I don't have to worry about hot shallow water (and crawdad destruction).
I started lilies this year too. I planted tubers in dish tubs about 4 inches deep in soil with sand and small rocks on top to keep tubers in place. I started them in water 4 inches above tub top. As they grew I pushed deeper into water they are now at 24 inches of water. I will leave them at that depth or a little deeper for the winter freeze then plan to pull shallow next spring and hopefully start cycle over again. I also placed fertilizer in pot while planting.