The order was put in place Wednesday and affected the Nova Scotia Community College Marconi campus and Cape Breton University.
The Environment Department issued a release Thursday saying subsequent samples have tested negative for E. coli and total coliform, and the order has been lifted.
Marconi Campus supplies the water for the university and as a registered water supplier with the province, must test regularly.
The department says positive tests can be caused by many factors, including testing errors or contaminated samples.
According to the department's website, total coliform bacteria is not likely to cause illness, but it indicates a water supply may be vulnerable to more harmful contamination.