Insert your shovel into the mud in a circular motion around the water lily plant. This will help loosen the roots.
Reach down into the mud to find the hard, tubular water lily rhizome. Pull the plant out of the water.
Wash the water lily roots with a garden hose. Pull off any soft root parts and damaged pads.
Cut the root down to 3 inches of rhizome, discarding excess roots. Retain the root parts that contain the best growth. Replace the roots you are keeping into the water and mud at a 45 degree angle.