(covers information from several alternate timelines)
A bathroom, also known as a restroom, toilet facility, lavatory, head, or refresher (also known, colloquially, as a 'fresher), was a room that generally contained a toilet, and could also contain any of the following: sink, shower/sonic shower, or a bath tub. These fixtures were then connected to a sewage and waste reclamation system via which waste products and water were recycled.
In 2255 of the alternate reality, Leonard McCoy sought shelter in the shuttle Bardeen's windowless bathroom in response to a bout of aviophobia he experienced. An officer later escorted McCoy, despite him voicing protestations, to a seat. (Star Trek)
In 2364, a series of malfunctions aboard the USS Enterprise-D – which were caused by a microbrain from Velara III – included locking two crewmembers in the head programmers' rest room. (TNG: "Home Soil")
According to the Star Trek: The Next Generation USS Enterprise NCC-1701-D Blueprints, the door in Jean-Luc Picard's ready room led to a bathroom. The blueprints also referred to the bathrooms as both "toilets" and "heads".
The main bridge of the USS Enterprise-D featured a bathroom just off the doors leading to the observation lounge. In the authorized re-creation of the main bridge in Star Trek: The Experience at the Las Vegas Hilton, the inscription on the doors read "HEAD". The head was visible in a few episodes, but while the doorway was initially labeled "CONFERENCE" in "Gambit, Part II", it was relabelled "HEAD" by "Emergence". In addition, in episodes throughout the seventh season, multiple crew members can be seen simultaneously entering the bridge via the head. It is unclear how many toilets are available for use in the head on the main bridge.
According to Jonathan Frakes during the "Journey's End: The Saga of Star Trek: The Next Generation" special in 1994, the Enterprise-D had only one bathroom. After stating that, Frakes proceeded to point to it on the large cross-section of the Enterprise-D in the main engineering set.
In the first draft script of ENT: "Shadows of P'Jem" (written while the episode had the working title "Untitled Andorians Return"), Trip Tucker noted that, in an extremely detailed Andorian map of a rebel compound on Coridan, the Andorians had "everything marked except the bathroom."