Japanese communal bath is a keystone in Japanese culture. They come from very simple to extravagance luxury bath with outdoor pools, but they all work the same way. Women and men bath separately (unless it's one of the few mix ones, which work differently). First you strip fully naked in the changeroom. Then you enter the bathroom, where there will be small shower hoses and mirrors along the wall. You take a stool, shower it, and sit in front of the mirrow. Here you wash yourself thoroughly (some baths provide soap, others don't, in that case, bring your own) and rinse equally thoroughly. Then you can join the other naked people (of your sex of course) in the hot tub. Some bigger places have multiple tubs with different temperatures and mineral enriched water.
Note that many places don't accept tattoos, since historically they were a symbol of connection to the Yakuza and other "anti-social groups".