Morecambe Road School was left surrounded by water when the floodwaters hit on Wednesday night.
The school was closed today, Thursday, as staff desperately tried to find ways of helping the water to subside.
Head Paul Edmondson said he and other members of staff were called into school at 6.30am this morning.
“The school grounds have completely flooded,” he said. “It’s up to 45cm deep in parts.
“The school itself is a little island in a field of water that’s not going away.”
Mr Edmondson said that while the school building itself was unaffected, water had got into ducts underneath the property as well as into the boilerhouse and some air conditioning units.
Pumps had been brought in to try to reduce the water levels.
“There’s so much water around the school that just isn’t going anywhere,” Mr Edmondson said.
“We had similar in 2015 [during Storm Desmond] but the main difference is that then the water subsided as quickly as it had risen.
“This time it’s not going anywhere.”
Mr Edmondson said the county council had been contacted to ask whether the new Bay Gateway had caused the problem.
The school, who caters for almost 150 children with special educational needs, will remain closed tomorrow, Friday.
“We are well aware of the impact this has on our families because they rely on our school a great deal,” Mr edmondson said. “We only make these decisions if we really have to.”