I have had some success clipping rasters with vectors using the tools available in a mosaic dataset.
In particular the 'Import Footprint Or Boundary' tool.
If you already have a shapefile defining 'water areas' then you could clip this out from the raster's footprint and then import it back in (joining by a field - I usually choose 'Name').
Before this step you would of course need to add your raster into a mosaic dataset (in a file GDB).
then export out the raw footprints using the 'Copy Features' tool, where in the screenshot below, 'test_md" is the mosaic dataset and '\Footprint' is the footprint of your raster.
Perform desktop clipping or editing functions in arcGIS Pro and import the raster back into the mosaic dataset with the option checked to 'build boundary'.
Also set the default option for clipping the raster to it's footprint and boundary in the Mosaic Dataset Properties (right-click on the mosaic dataset in the file GDB).