Trolls won't destroy a properly sited ocean base. I suppose serpents might but their spawning rules seem to be based on a viking actually being in an ocean biome.

An alternative, in the case of trolls, is to have "walls made of cannon balls." An active defense. Shoot trolls, stay within their sight range. As long as they are chasing you and you keep several meters away from your Base structures, trolls will chase you and ignore your base.