Three officers were taken to hospital for treatment and 13 people were arrested after separate clashes in Belfast and Newtownabbey on Friday night.
Rioting in Belfast took place in the busy Shaftesbury Square area, near Queen's University, and in the areas of the Crumlin Road and the Ligoniel Road.
Traffic was severely disrupted as around 200 people gathered in Shaftesbury Square shortly after 7pm, carrying Union Flags and blocking the road.
Police confirmed trouble flared after a man tried to drive a black van through a roadblock.
Police said the vehicle was driven "erratically" in the area.
"The keys of the vehicle were removed by a member of the crowd. Police have moved the vehicle and the motorist to a safe place," a PSNI spokeswoman said.
Bottles and other missiles were thrown at police during the disturbances, while a car was hijacked in Stroud Street off Sandy Row and set on fire. A parked car in Donegall Pass was also torched by rioters.
"The water cannon was deployed to the Donegall Pass area for a period of time, but has since been removed," police said.
Police have confirmed Shaftesbury Square has now reopened to traffic.
Three men aged 18, 29 and 41 were arrested for riotous behaviour in the Sandy Row area, while a third arrest was made in the Donegall Road area for disorderly behaviour and obstruction.
A 13-year-old boy was arrested for riotous assembly in the area of Legann Street in north Belfast.
I am urging everyone to be calm, take a step back and think about how this violence is affecting not just their own communities but the whole of Northern Ireland.
Assistant Chief Constable Will Kerr
The water cannon was later deployed and used in the O'Neill Road area of Newtownabbey as a crowd of around 70 people blocked the road and attacked police with bricks and masonry after 11pm.
Two petrol bombs were thrown at police vehicles. A number of police vehicles were damaged during the disturbances.
Four men aged 19 and three men aged 22, 18, 17 and 16 were arrested in the area.
Police also responded to reports of a number of vehicles being set on fire in the Carnmoney Road North area of Newtownabbey close to Mossley Mill.
On Friday night loyalist demonstrations also took place in the greater Belfast area, Bangor, Enniskillen and Dungannon.
The latest trouble erupted in the wake of a Belfast City Council vote which restricted the flying of the Union Flag over City Hall to 17 days a year.
Nationalists wanted to remove the flag altogether but the Alliance Party, which holds the balance of power, put forward the motion which was passed.
A total of 27 police officers have been injured in rioting since Monday's vote, while a number of Alliance Party representatives and properties have been targeted.
Assistant Chief Constable Will Kerr said: "This behaviour is simply not acceptable. These people are only wrecking their own communities and putting innocent people's lives at risk.
"This mob violence and intimidation cannot be allowed to continue and I am urgently appealing to politicians and those with community influence in these areas to do what they can to put a stop to this behaviour now before someone is seriously injured or killed."
ACC Kerr said those responsible will be brought to justice.
"My colleagues are providing a very strong presence and robust approach to this violent disorder and I can assure members of the public that we will not tolerate any form of criminal or violent activity," he said.
On Friday outgoing US Secretary of State Hillary Clinton spoke out against the violence.
She met First Minister Peter Robinson and deputy First Minister Martin McGuinness at Stormont Castle before returning to America at the end of a brief farewell European tour.
There are plans for a major protest in Belfast city centre on Saturday afternoon - which is expected to be the busiest shopping day of the year.