Exhibitions team leader Jennifer Evans said the flood was discovered at 7am, but swift action by the museum's emergency response team meant damage was minimal.
The team, specialist contractors and museum volunteers spent much of the day mopping up, and setting up about 50 fans and dehumidifiers to help dry the area.
About half the 1500sq m floor area of the new collection store was flooded.
The facility was completed in November 2009 and meets international standards of collections care, with a fully controlled environment and state of the art storage racking and object processing facilities.
Ms Evans said damage to the collections and the new building was minimal because the new storage units, stillages and shelving meant none of the collections was on the ground where the water collected.
The collections are safe and current assessment suggests only two collection items would require further treatment in the museum's new conservation lab, Ms Evans said.
Museum director Linda Wigley said seeing water everywhere when she arrived at work was her worst nightmare.
However, she was proud of the response of those involved in the clean-up.
"It was literally all hands to the pump.
"It was so encouraging to see all the emergency planning, training and staff expertise put into action to avert what could have been a catastrophe.
"You plan and hope, but never know how people will react until the balloon goes up."
Ms Evans said all water was expected to have dried up by today.
