The section of road between Aotea Quay and Ngauranga, which carries 90,000 vehicles a day, is having another northbound lane added.
It will also run a system where operators use a network of cameras and alter the speed limit depending on how busy the road is - slowing the traffic in peak times to spread out the number of cars heading to exits.
The New Zealand Transport Agency's Wellington Highways Manager, Rod James, says reducing speed limits will allow a smoother traffic flow and get more vehicles through faster.
He said the work will be carried out on 1km sections of road at a time and the limit will drop to 70 km/h in those areas.
For Kapiti, Wairarapa, Porirua and Hutt Valley commuters the road is the doorway in and out of the CBD.
Mr James said there were high demands on the 3km stretch of road making it an ideal spot for the $50 million project.
"The smart motorway concept is about controlling the speed of traffic as it flows through a busy section - reducing the speed limits before congestion occurs.
"It allows us to get a smoother more managed flow and by doing that we get more traffic through the same amount of road than we otherwise would."
The Automobile Association expected the system to work well when it was up and running. Spokesman Dylan Thomsen said a lower limit would stop people speeding towards their destination and clogging up exits.
But Mr Thomsen said the system had not been used in New Zealand before so the NZTA needed to sell it properly to drivers.
"If they don't know that the speed limits are actually being managed to make sure everybody gets there as quick as possible and the flow is better - if all they see is a lower speed limit than they're used to and the roads looking pretty clear ... then a lot of people would probably be confused by that," he said.
"[Drivers could] think that the system wasn't working right."
Among the physical changes would be a narrower median barrier, freeing up room for a fourth northbound lane.
Squeezing in that extra lane meant losing the motorway's shoulder, but the NZTA says if people broke down they could use new stopping bays and if drivers could not get to them, traffic operators would close lanes until help arrived on scene.
Wellington City Councillor Iona Pannett expected the system might have teething problems because changing speed limits could confuse drivers.
"When you implement a new roading system it can take drivers some time to adjust," she said.
"I think NZTA will have to explain very carefully how no one is going to get hurt or killed while drivers get used to a new system."
The NZTA said the roadworks would make journeys slightly longer in light traffic, but would not make much difference during peak times. Lower speed limits on various section of the road would be in place until March next year.