The Bellville campus student centre and parts of the administration building at the Cape Peninsula University of Technology had to close after they were flooded on Friday morning.
The flooding is suspected to have been caused deliberate. A student has been arrested, GroundUp reported.
University spokesperson Lauren Kansely said: "The building will remain closed until deep cleaning of the space has concluded. Access times to the venue will be reevaluated once it reopens.
"The reason for the flood is being investigated by SAPS and one suspect has already been arrested, with more arrests expected to follow in due course."
Students without accommodation, who had been occupying rooms there, have been affected by the flooding.
"The sabotage of institutional infrastructure affects innocent students' right to use the facilities and services they require," said Kansley.
"We are still waiting for the housing department to assist us, and now there is water," said analytical chemistry student Asiphe Maholo.
"The university now has reasons to ask us to vacate as the building is unsafe to be occupied. The person who did this cost us a roof over our heads."
The SRC, which is led by the EFF, declined to comment directly on the matter.
Its secretary general, Sihle Ngxabi, said: "Our students are losing patience and, once they totally lose it, there are no guarantees. We, as the central SRC, are also losing patience because our masses are getting the impression that we have lost our radicalism; too diplomatic in approach and taking time to solve problems.
"The truth of the matter is that we are exhausting all diplomatic processes so that there is no one to blame when things get sour."