Hi Peter
You can test and I hope that you succeed! If so, please give me your tricks. I do not want to deceive you in advance but, however, I tested something similar, with polarising filters and, even considering that you can eliminate all the reflections, you have the water refraction angle. If you tilt the camera over the photographed area the angle change by the air/water fluids will completely fool agisoft Photoscan or any other photogrammetric software. The only possible way is to do the photos completely submerged. From the air, if the water ripples slightly (I do not even talk about small waves), the refraction will completely destroy your 3D model.
Cheers