"Sento" refers to public bath, while “onsen” refers to the use of natural water. For example, onsen will usually be within a hotel in a destination with naturally heated water, such as Hakone or Arima onsen.
What is the best sento in Tokyo? In my opinion, the best one is the one near your house. People in Tokyo spend enough time commuting to work, so I would recommend a visit at any local sento. However, if you are not sure where to go, I can recommend the following:
“Minami Aoyama Shimizu-yu” near Omotesando station is well-located and they have slightly larger than usual baths. They are closed on Friday. This is their website. It is a slightly nicer version of the typical sento.
If you would like to experience special and natural water in Tokyo, you can try “Take no yu” near Azabu-Juban station. Their water is naturally black and leaves a soft feeling! They are closed on Monday and Friday. This is their website.
If you have tattoos, most public baths will not allow you inside because in Japan, tattoos are linked to organized crime. I would suggest “Bunka Yokusen” one station away from Shibuya (Ikejiri-Ohashi station). They are open every day until 1 am, as well as Sunday morning for "asa furo" (morning bath). This is their website.
Although it may take some getting used to, I recommend spending one hour at the sento. I would take my time to clean myself thoroughly using a bath towel and soap, perhaps brush my teeth, and then alternate between the hot and cold bath (it is not very cold and actually more relaxing than the hot bath in my opinion). Using the sauna requires an extra fee that can be between 300 and 500円. You can rent a towel and buy shampoo and bath soap.
The first time I went to a sento, I remember feeling annoyed that I had to wash myself before taking a bath on a small chair that was not comfortable. However, this feeling goes away quickly and taking your time to wash yourself while comfortably sitting is an enjoyable part of life in Japan after a long day at work.
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