ANU security staff were called to Sullivans Creek on campus after more than a dozen people were found rafting down the flooded waterway.
Police were also called to the creek to stop the rafters, but the rafters left the scene before police assistance was needed.
A video clip posted on the internet shows three rafting boats, with two to four people in each, rafting down the flooded creek.
The university's vice-chancellor, Ian Young, warned people of the ''dangerous activity''.
''This is a highly irresponsible activity in the circumstances,'' Mr Young said.
Mr Young said Sullivans Creek was full of muddy stormwater and strong currents, as well as hidden hazards such as fallen tree branches, rocks and floating debris.
Many of the rafters fell into the creek after their raft became lodged in rocks.
''The people involved in yesterday's actions are extremely lucky they did not cause themselves, or others coming to their aid, serious injury or worse,'' Mr Young said.
''ANU security will be monitoring use of Sullivans Creek over the weekend given the potential for repeat flooding.''
Police said the dangers of entering flooding water was highlighted on Thursday night when police officers rescued a 43-year-old man who jumped from Queen's Bridge on Monaro Street in Queanbeyan.
Police were called to the bridge at about 11.20pm after the man threatened to harm himself.
They lost sight of him after he jumped from the bridge into the flooding Queanbeyan River and was swept downstream.
Two police officers entered the river to find the man. One of the officers was able to free himself after becoming entangled in a submerged fence. The other police officer was swept downstream but was later found. The 43-year-old-man was found clinging to a tree 500 metres downstream and was rescued by Queanbeyan SES volunteers.