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:
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: