Smithills School was forced to close for the day after the heavy flooding on Smithills Dean Road and Moss Bank Way.
Only about 60 out of 1,600 pupils managed to struggle in and floodwater came within an inch of affecting the upper school building.
Head teacher John Lawson said: "The decision to close the school was taken in the interests of pupil safety when the police decided to close Smithills Dene Road.
"Not only were pupils not able to get in, but we would have had a problem if there had been an emergency because the emergency services could not have got through."
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