Creating a 3D model depends upon identifying the same feature in multiple photos. Since water can have a featureless surface, it often does not show up in the 3D model. Thus maps derived from the model will be blank in these areas. I do not know what you can do to fix this on your existing set of photos. There may be other settings in the photogrammetry software that could recover more of the area but this would require custom settings and much more processing time. I could try processing your photos with different settings in a different program if you feel comfortable sending me a link via a DroneDeploy message to my userid. To do this, just click on the S in the brown circle above and select Message.
Not only is water featureless, but it is in constant flux between images. So, there may not be any, or very few tie points for software to work with.
Contiguous images of open water water will typically create processing issues in all photogrammetry applications. Its not specific to DD, but in Pix4D or Agisoft you could try to place some manual tie points to help the computer.
Are you mapping sea grass? I’ve met some people in Tampa who do it and I’ve always wondered how they handled water. I’d guess the shallow water would reveal some tie points for the software to work with but obviously not here.
Easily explained like @Dave mentioned. Constantly in flux makes it impossible to create tie-points. The only weapon against this is getting additional images from a much higher vantage point so that you can try to capture bank-to-bank.
When mapping over water, conditions have to be just right. The water has to be clear enough you can see the bottom and the bottom has to have some features. Just sand won’t usually work. It also has to be fairly calm and the sun angle has to be just right. Earlier or later is better so you don’t pickup all the sun glare in the images.
I’ve gotten the best results mapping over water with Drone Deploy compared to Pix4D, AgiSoft, and Drone2Map.
Earlier is always better. End of the day sun is harsh. Higher is better. Any semi-static feature will stitch to a point, but close enough to model without missing areas, pits or spikes.