The toll was to end in 2003 once the bridge and tunnel were paid for
Toll charges are to be increased by up to 50% for the Dartford crossing over the Thames between Kent and Essex.
The new Dartford Tunnel and QEII bridge fees, which include free access between 2200 and 0600, will be officially introduced at 2200 GMT on Saturday.
Day-time crossings will rise from £1 to £1.50 for cars. Lorries will be charged £2 or £3.70, depending on their size.
However, local car drivers will be able to join a scheme for 50 free crossings and a 20p rate for subsequent uses.
The discount scheme is available to people who live within areas covered by Dartford and Thurrock councils.
Residents in Dartford and Thurrock, Essex, will get the free journeys after they pay a £10 registration fee for an electronic tag, known as a Dart-Tag, to display in their car's windscreen.
Other users of the Dart-Tag will be charged £1 for a crossing by car, £1.75 for two-axle goods vehicles or £3.20 for multi-axle goods vehicles.
A spokesperson for the AA said they were concerned the free access at night would add to congestion as drivers rushed to cross the Thames before 0600 GMT.
The toll was to end in 2003, by which time the bridge and tunnel had been paid for, but was kept on by the Department for Transport (DfT) as a congestion charge.
The DfT said an independent report in 2001 showed that without charges, traffic would increase by 17.1%.
More than 7,700 people have put their names to an online petition against all charges on the route on the Prime Minister's website.