Pirate, Short of putting some unmoving markers in the water, I don't know of a quick fix. I'm no expert at water and land banks and all that but Photoscan will not recognize moving elements, and water is moving all the time and reflecting and essentially changing its form constantly.
Unmoving markers that are anchored to the land under the water would help you. Then Photoscan could grab those items. But they can't be floating (and therefore moving) or you will have the same problem as you are currently having.
Maybe someone with some more experience with the type of project that you are trying to do will be able to pass on some tips in addition to mine.
Jon