Water, when viewed through barrier blocks that are directly over it, will be invisible. However, from the sides or below it will appear, and if there is air above between the water and barrier or if the water is flowing, it will appear. The same applies for lava. Also, barrier blocks can be waterlogged, and sea grass and kelp can grow on them, If they do grow on it, the water block they are occupying will turn invisible.
I'm not sure if these features are bugs or intended features.