"It's the girls' toilets!" -- Harry Potter (PS10)
This bathroom is where Hermione goes to cry after Ron is mean to her on Halloween. While looking for Hermione to warn her of a troll that has entered Hogwarts, Harry and Ron see the troll enter a room on the first floor. The boys lock the troll in, only to realize that they had just locked it in the bathroom with Hermione. Harry and Ron rush in to protect Hermione and they manage to knock out the troll, before being found by McGonagall, Snape and Quirrell.
The novel does not say specifically which floor this bathroom is located, but Percy does lead Harry, Ron and the other Gryffindors from the Great Hall up a flight of stairs. Then Harry and Ron "joined the Hufflepuffs going the other way, slipped down a deserted side corridor and hurried off towards the girls' toilets. They had just turned the corner when they heard quick footsteps behind them." This shows that Harry and Ron were currently on the floor of the bathroom, then:
"'Percy!' hissed Ron, pulling Harry behind a large stone griffin. Peering around it, however, they saw not Percy but Snape. He crossed the corridor and disappeared from view. 'What's he doing?' Harry whispered. 'Why isn't he down in the dungeons with the rest of the teachers?' 'Search me.' Quietly as possible, they crept along the next corridor after Snape's fading footsteps. 'He's heading for the third floor,' Harry said, but Ron held up his hand." The only way they would know that Snape is heading for the third floor is if they were on either the second or fourth floors.
Because Snape was coming from the Great Hall / the Dungeons, it is most likely that the bathroom is located on the second floor.