Its the way the terrain is generated, instead of blocks of voxels, the game uses a line geometry... a line for sea level, a line for terrain with rocks and ore chunks buried into the terrain lines, this makes for faster terrain loading but limits the interaction between terrain and sea.

In brief this happens because the sea terrain is coded to lift and drop during storms, and as such there is not that level of detection for terrain collision... that would up the requirements by a tonne.