It took just over an hour to get rid of the water.
Shore Care Accident and Medical Centre, which sits opposite the hospital, was notified of the flooding.
A Shore Care spokeswoman said they were warned by North Shore Hospital that they could have a few patients heading their way.
She said Shore Care shared a good relationship with the hospital.
"We're here to support them and we hope they'd do the same for us."
A doctor was called in early to help attend to the patients who arrived from the ED.
Shore Care couldn't disclose the seriousness of patients' medical conditions they saw from the ED due to privacy issues.
The ED was up and running again by 1.30pm.
Waitemata DHB reported that damage to the ED was minimal and there would be no disciplinary action taken.