Teachers and parents at Tawa primary school have spent the day cleaning up after yesterday's rainstorms left four classes unusable.
Principal Ian Dewar said the school had to ferry its littlest children to higher ground in inflatable boats.
He said the whole centre of the school was between knee and waist deep in water.
They were forced to use boats from the on-site swim school to ferry the five and six-year-olds to safe ground, Mr Dewar said.
"The other three main blocks were completely surrounded so we had to use boats to get the children out of the classrooms and up to the higher part of the school so that was pretty exciting.
"Out of about 300 kids, most of them found it a pretty exciting experience, loved it, will be talking about it for months."
Mr Dewar said sewage may have contaminated the classrooms, which could delay relining them until term three, forcing children to be housed in temporary classrooms for the rest of the term.
Meanwhile businesses in central Tawa spent the day drying out sodden floors after the flood.
Nada Bakery owner Michael Gray said the drains were upgraded just last year and should have been able to cope with the water.
"The drains that we've got out the front here just aren't adequate. They did say they had upgraded them - they did some work on them last year, but ever since they've upgraded them is when we've actually had flooding. We haven't had this in the five years we've been here."
Mr Gray said the business owners would have hard questions for the council, however, Wellington City Council spokesperson Richard Maclean rejected the suggestion the drains were at fault.
"We don't agree that yesterday's flooding was related to any drainage improvement works that we've done.
"Yesterday's flooding was caused by the heaviest rainfall in the Tawa area in the past 40 years.
"It was probably the worst flooding event since 1976.
"There was just an overwhelming amount of water ending up on the low-lying land in Tawa."
Mr Maclean said the council spent tens of millions on upgrading the drainage system in the region, including Tawa.