I have noticed small black dots covering to tops of the lily pads, looks like aphides?

The majority of water plants are relatively pest and disease free, so it more than likely is aphides, they are easily removed. Depending on the size of the area and the amount of aphides presents, (lets assume a heavy infestation in a 2m x 1m pond) throw about 2 to 3 tablespoons of olive oil over the pond surface, then spray vigorously with a hose or bucket, using enough force to disperse the oil across the top of the pond and push to leaves underwater, thus washing off the aphides. The aphides will suffocate from the oil and the fish will have a tasty meal.