Police had tried to storm the campus of Hong Kong Polytechnic University overnight.
Many protesters wear masks to shield their identities from surveillance cameras that could be used to arrest and prosecute them.
Witnesses saw some protesters suffer burns from chemicals in the jets fired from police water cannons, according to Reuters.
On Sunday night, police tried to enter the university but were forced back by protesters who set huge fires.
ABC China correspondent Bill Birtles was at the scene and described what he saw as "all hell is breaking loose".
The Polytechnic University protesters had been blocking one of Hong Kong's major highways, the Cross Harbour Tunnel linking Hong Kong island to the Kowloon peninsula, for much of the past week.
Escalating violence between anti-government protesters and police in the former British colony has been condemned by Beijing and the city's Beijing-backed leaders. »