Applying Water Breathing when having Breath of the Nautilus has no effect.

Water Breathing should refill bubbles, while Breath of the Nautilus does not.

However, logic dictates that water breathing is stronger than breath of the nautilus, thus should refill bubbles. However the inverse is true, the breath of the nautilus pausing bubbles is overriding the water breathing causing your water breathing potion to be wasted when riding nautilus.