Matt,
We used two different sensors, so there are two distinct point files for water depth. The idea was to transect back and forth across the trench to include the unaffected, adjacent reference plane. As you'll see, the transects are little haphazard. I included a polygon file as well that could be used for clipping, as I did for a TIN and contours
You should notice that the general bottom topography trends deeper to the south, with the incised trench superimposed over that general pattern. This is why any approach that uses a level baseline plane won't seem to work. I hope you have a suggestion.
Cheers,
Mike