Welcome, Rev,
A deep pond is a GOOD pond! I tried to get mine t 36", but in the Houston gumbo clay soil, could only get a small 3'x3' section that deep; the rest is 30". For fish, especially koi, the deeper the better. Deep water keeps the temperature stable, plus gives fish the option of swimming up and down, instead of just back and forth. Up and down builds muscle better than back and forth. Deep water also allows fish to escape predators.
Lilies want only about a foot of water over them. So try putting them up on upside down milk crates. In addition, the crates provide hiding places for your fish. I cut some of the plastic lattice out, so the larger fish can get inside.