I have started the pond areas by surrounding them with a dense layer of trees. I keep the center of the area free to generate the body of water and dirt or mud area. Sometimes the dirt area takes over the whole center during generation which can cause it to seem like the water has dried up which was an unexpected but nice effect. I have set the cat tail plants to spawn around the waters edge. The monster head looking thing in the deeper water is an entrance to a water dungeon.
I increased the water and made it run through the grass and dirt to create a marsh like biome. This is working well so far.