Sveral lilly pads, all of our fish are showing up dead.

Be surprised if the lily pads are the culprit. I'd suspect water chemistry or too much heat and not enough dissolved oxygen..

How large is the pond (gals.)? How many koi and what size are they? Also, what kind of filtration and what is the size of your pump? One last thought, how much do you feed and how often a day?

I agree with ma0641. It's not the plants.

It is most likely to be the lily pads as during the day the give oxygen to the fish, but in the night this doesn't happen which causes the fish to fight the lily pads for the oxygen. This usually results in fish dying during the night.