The alerts have been condemned by local politicians claiming those behind them were trying to raise tensions in the city.
The railway station remains evacuated following reports that a suspicious object was left in the area.
Quarry Steps at Spencer Road in the Waterside of the city is also still cordoned off in a separate alert.
The railway line between Coleraine and Derry has been closed while searches are carried out.
A bus substitution service is operating between the part of the line that is closed.
The pick up point in Derry will be at the bus centre, not the railway station.
Passengers for Ballarena and Castlerock will be bussed to and from Coleraine.
Chief Inspector Tony Callaghan said: “Cordons are in place, and the Foyle Arena has been opened for anyone inconvenienced by the alerts.”
SDLP leader Colum Eastwood said the bomb alerts, along an Apprentice Boys parade route, were an attempt to raise tension and “diminish our peace”.
“Those who seek to disrupt that respect or diminish the process of reconciliation in this city with bombs or bullets have betrayed the people of Derry,” he said.
“This is not about a divide between Catholics and Protestants, unionism and nationalism or loyalists and republicans.
“The only divide in this city is between those who want to blow our peace apart and those of us who will stand together to protect it.”
Sinn Féin assembly member Raymond McCartney said the alerts “do nothing for the image of the Derry as a forward looking city”.
“They have also caused disruption to city centre traders who were already experiencing a slower than usual day in the run up to Christmas as a result of the Apprentice Boys parade,” he said.
“Great strides have been made in recent years by the local community, the Apprentice Boys and the PSNI to ensure a respectful atmosphere and minimise disruption, and those efforts have been widely supported.”
DUP Foyle MLA Gary Middleton said the alerts “will have inconvenienced many local people and visitors to our city today, but they have achieved nothing”.
“Derry suffered enough at the hands of those who want to drag Northern Ireland back,” he said.
“The contrast between the positive work done by the Apprentice Boys and those who want to create disruption and fear could not be greater.”