We were actually looking at this job just because the water was so clear.
1. When you are around water like this it can make the model do a lot of weird stuff. You actually had quite a few reflections in the images and I am surprised it turned out as well as it did. Almost every image had a sun glare in it.
2. Full 3D processing is definitely not what to use here. It is very aggressive with its filtering in an attempt to clear up overhanging areas.
Any time you are mapping around water you should use a circular polarizing filter to block some of the glare and increase contrast.
You would likely be better off mapping either earlier or later in the day to get the sun glare out of the camera's field of view. Or a cloudy day but that wouldn't look as cool.