I had put stonewalls under the water around my base just high enough that you can hardly see it, but you can't swim over it.. Mods make(according to my experience) less damage in water to structures. At least two troll attacks in the water, on my stone walls have made as good as no dmg.

And for the rest, I just go out and fight the mobs. No (in my opinion) ugly moats or plateous necessary.