Nakabusa Hot Spring in Azumino, Japan offers a traditional hot spring experience with 29 natural springs to soak in. While the buildings and facilities may be a bit run down, the outdoor onsen has one extra element that is quite unique for Japan. There is a large swimming pool style where you could literally do short laps in the hot water and feel the minerals under your feet in the chest deep water.
You can visit here on a day trip with the details currently being:

Bathing Reception Hours: 9:30 AM - 4:00 PM 
(Facility Closes at 5:00 PM)
Price 950 yen/one person

If possible, try enjoy staying here overnight to make the most of all the onsen for 24 hours and head out at night to be under the bright stars in the dark mountain skies.