The flood, which started from a burst pipe under a sink, was discovered when a teacher went into the school to drop off a box just a day before they should have been going back to school, in September.
It meant that three of the classes, comprising 54 children in total, had to suddenly relocate to Hawsker-cum-Stainsacre School to study.
It took the entire autumn term for Fylingdales School to dry out and this was followed by refurbishment work before pupils were finally allowed to return after the Easter holidays - more than seven months after the incident happened.
For Helen Thompson, executive headteacher of The Heritage Coast Federation which covers both village schools, it wasn't exactly the dream start to her new role so she is glad that normality has now finally returned, especially after all the previous disruption caused by the pandemic.
"We invited parents to come in after school to have a look round and see how everything is now it's been reinstated," she said.
"We wanted everyone to be welcomed back into school again so it was an exciting day.
"Some of the children said they felt quite bittersweet as they had formed some good friendships at Hawsker.
"They were excited about going back to their school but they had built friendshops in the other school.
"The Hawsker community welcomed us with open arms.
"We didn't anticipate it was going to be for so long - we can't thank them enough."
Mrs Thompson praised the "creativity and dedication" of the federation's staff in making the relocation possible.
She also praised the resilience of the pupils affected.
"There was one class that stayed on site at Fylingdales, in a prefab," she said.
"That was hard for them as that was just one class on their own throughout."
"They didn't have the rest of the school community there with them, so we've been very fortunate that Whitby DAG supported us and we hired their minibus to transport children between the two sites."