Water lilies are usually started in one or two gallon pots. A four to five gallon pot is better if the pond has space for larger pots. A four and a half-gallon pot measures sixteen inches in diameter by seven inches deep.A wide shallow pot matches the growth habit of the spreading root system of a water lily.ater lilies must have a minimum of ten inches of water over the soil surface in order to bloom. Deeper water keeps the root system cooler and shaded, encouraging better growth and flowering. Most lilies perform best in water depths twelve to twenty four inches.