Underwater surveying projects are considerably harder compared to the regular indoor/outdoor image acquisition procedure due to the very hard environment conditions (viewing distance is limited, controlled light environment is almost not applicable, difficult to place and fix even a few control points in scene, may be hard to repeat the operation). Therefore we recommend to plan the survey carefully before performing actual shooting session. Taking more images than needed is always better than having insufficient image overlap or incomplete dataset.

If possible wait for the calm weather and bright light - it will allow to increase the visible distance.

Consider using lighting when shooting underwater or a constant source of light that will increase the visible distance and quality of the obtained images.

We can recommend a survey using a "snake" or "spiral" route as shown in the image below: 

If the image data is acquired from the video sequence and the EXIF information is missing, set camera sensor parameters - focal length and sensor pixel size (both in mm) in the Metashape before starting any processing operations. Set parameters via Tools Menu > Camera Calibration dialog according to the camera/lens specifications:

Starting from Metashape 1.7.0 version will be able to see what large blocks the alignment has grouped, without having to transfer the cameras to a new chunk and re-align. It features the name - Components concept. This will allow you to analyze the problem faster and use markers to align components with each other, for example, if Align Selected Cameras doesn't work in most cases. 

In some underwater case, we can suggest trying to align photos using Reference settings - Sequential and, after that, align photos using Reference settings - Estimated.

In case the camera track followed the single straight line (without multiple lines and side overlap) we can suggest using Sequential preselection option in the Align Photos dialog and disable the Generic preselection option. 

Reference links for additional information:

1. Shaun Lee, "Mapping life on the seafloor". September 04, 2020 

2. Deep3D, "Aligning The Images – Why Things Go Wrong". March 08, 2019

3. M. Abdelaziz and M. Elsayed, "Underwater photogrammetry digital surface model (DSM) of the submerged site of the ancient lighthouse near Qaitbay Fort in Alexandria, Egypt". May 2019

4. E. Diamanti and, F. Vlachaki, "3D recording of underwater antiquities in the south Euboean Gulf". April 2015

5. M.O. Zhukovsky, V.D. Kuznetsov , S.V. Olkhovsky, "Photogrammetric techniques for 3D underwater record of the antique time ship from Phanagoria". September 2013