Hashtag’s Guide to Water-Capables mentions frequently that a ships beam weapons can’t be used on submarine units. The beam's Shockmancy won’t penetrate the surface of the water.WB2014 Duke Forecastle - Part 23 The recommended tactic is to use Harpooners to attack them, since their harpoon's can penetrate the water's surface and damage them.
Known Subrmaine Units include:
It's possible not all Aquatic units are Submarine units. For example, aquatic units like Wake snakes and Groovesharks have been hit by Beam Weapons, so unless they can go far under the surface they must not be Submarine units.WB2014 Duke Forecastle - Part 5
Potential Subrmaine Units: