One of Hokkaidou's most spectacular ocean-side baths, Mizunashi Kaihin Onsen is simple and pure, and only usable when the tides are low: each cycle the high tide covers the baths, so you have to be there at the right moment to bathe.  Timed right, it's a wonderful soak, though there were some small crustaceans that were biting at the time the author took a dip.  There's a small changing area, but any bathing is entirely in the open, so this isn't a good option for the bashful.  You are, apparently, allowed to wear a yukata or swimsuit if you choose.  The baths themselves vary in te

On the shore of Tachibana Bay, Obama Onsen makes a wonderful day trip from Nagasaki or a nice stop-n-soak on the way from Nagasaki to Unzen or Shimabara.  There are several baths, the nicest of which is right next to the water.  You can higaeri or stay overnight at some of the inns.  It's a small spot, without much else to do, but that's part of the charm here.  Just get away from it all.