There are only a few diseases that affect aquatic plants, the main one being fungal leaf spot. One attacks waterlilies and causes spots on the leaves that sometimes develop into dark patches and dry, brown edges. The affected leaves should be removed by hand as this is the only alternative to spraying with fungcides, which is not an option if there are fish in the pond.
Irises can also get leaf spot, it shows itself as random brown spots that sometimes elongate into brown streaks following the direction of the veins. Leaves can be removed as before, however, if they are far enough from the water to prevent any drift a wide-spectrum fungicide can be used if the disease is caught early enough. Follow manufacturers instructions and used on a very still day.
Waterlilies can ocassionally get a lethal form of rot that affects the crown. First signs are the yellowing of the leaves, then the leaf stems turning brown and begin rotting. The whole plant will look extremely sick and when removed from the water will give off a vile smell, from the rotting, soft and gelatinous roots. There is no cure for this and the plant will have to be discarded. If there are fish in the pond you may have to do a water change as the rotting plant will have fouled the pool and depleted the oxygen levels.
The most common disease is mildew and it it particularly seen on calthas (marigolds and kingcups). A solution is fairly simple however, cut all the foliage away completely and the plant will usually grow back without mildew.
Water snails are common in most ponds but where there is ample foliage their presence is not a problem, and damage hardly noticeable. If they do get to be a problem try floating a lettuce leaf on the surface in the evening, the following morning you should find snails underneath the leaf. This will only work in ponds without fish as they, particularly koi, will eat the lettuce.
