One of the top three onsen towns in Japan is Gero Onsen in Gifu Prefecture. It’s a lovely river-side city with many onsen to visit. If you venture little ways up the mountain away from the river, you can visit the onsen temple, Onsen-ji.
One story form Gero Onsen’s history of over 1000 years is this. In 1265, the onsen’s hot water stopped. The following year, the villagers noticed a the flashing white wings of a white heron dancing on the riverbed of the Hida River every day. When they went to figure out why the heron kept coming to the same spot, they found onsen water flowing up out of the ground.
The heron flew up into the sky and to the trees a distance from the river. There, shining under a pine tree they saw a shining figure of Yakushi Nyorai and built the temple at that spot.
The temple is a very quiet, peaceful spot surrounded by trees. No one was there when we visited, but a small stack of pre-written and stamped goshuin were available with a place to put 300 yen.
It is accessible via stairs up from the city or by car. There is a parking lot a little further up the mountain near Yunoshimakan.
Homepage: http://www.onsenji.jp/ (Japanese)