Hillcroft Special School has been closed for almost a month after legionella bacteria, which can cause legionaries' disease, was found in an unused shower block.
The North Eastern Education and Library Board closed the school as a precautionary measure to allow for extensive works to take place on its water system.
The board said a new treatment system has been put in place and has reviewed maintenance procedures.
A statement from the NEELB said: "The board regrets the disruption that has taken place to the educational routine of the pupils who attend Hillcroft School and is delighted to be in a position to re-open the school.
"We very much appreciate the work of the principal and staff during this difficult period and would wish to express our thanks to parents for their understanding and support."