The most common pests are Water Lily Aphids the Water Lily Beetle and the China Mark Moth. Tempting as it may be we would not recommend using any insecticides you can get from your garden centre, especially if you have fish in the pond, but even if not they may harm other beneficial aquatic life.
Water lily aphids are sap-suckers very similar in appearance and size to the vegetable blackfly and form dense colonies on the underside and top of the pads and top of the petioles (stems). Lilies are particularly prone to attack where they are overcrowded and the stems and leaves stick out of the water. Prolonged attack will cause yellowing and curling of leaves and destruction of buds and flowers. Control by hosing down the leaves and stems and squashing and rubbing off with fingers. They can also be drowned by dropping the lily down so leaves are submerged for a day or two.
Water lily beetles are small brown beetles whose larvae strip the surface layer of tissue from the pads creating holes and causing the leaves to shrivel and die. Adult beetles also feed on the flowers. They hibernate over winter in poolside vegetation so cutting down herbaceous plant material in autumn will remove their winter protection. Leaves should be hosed down regularly to remove larvae, and adult beetles and larvae can be removed by hand.
The tell-tale signs of the China Mark Moth are oval shapes cut from the leaf margins. These are used to stick to the underside of the pads to cover themselves while sleeping and eating the underside of the leaves. They tend to cut new pieces each day so cause extensive damage. Check underside of leaves and squash the protective cases and brush off. Alternatively remove the effected leaves and burn.
Water snails are thought by some to be a problem, but generally they seem to prefer dead and decaying leaf matter and algae rather than fresh healthy leaf growth so on balance should be beneficial for your pond. The two most common are the Giant Pond Snail and Ramshorn snails commonly sold to pond owners. In reality snails will naturally colonise your pond either introduced with pond plants (the jelly strings often stuck to the underside of leaves), via visiting bird life or trekking in from nearby water habitats, so rather than buy them with a little patience they will soon start to appear.
Dragonflies are most definitely not pests but mentioned here to help dispel the myth that they harm plants -they eat bugs and are great for a pond, as well as being fascinating and beautiful (well, ok, the larvae wouldn't win any beauty prizes...) insects.
The first symptoms of Water lily Crown Rot are yellowing leaves which sometimes become mottled. The leaf stems then become soft slimy and blackened and later break away from the crown. The crown itself will be soft and gelatinous with black tissue inside and will have a vile smell. The only way of dealing with it is to quickly remove and destroy the infected plant as it can and will spread to any other lilies in your pond. If other lilies remain unaffected after a few weeks to a month then it is safe to replace the lily.
Water lily leaf spot is more common but less serious than crown rot. Pads will develop concentric red or grey-brown spots on their upper and lower surfaces and eventually rot. Disfiguring but not serious so just remove any affected leaves as soon as they appear.