In the city, some parts of Tamaki Drive could also flood, the transport agency warns.
The agency's national journey manager, Kathryn Musgrave said the king tides would be at their highest on Saturday and Sunday morning.
"Our advice to all road users, including cyclists and walkers, is to take extra care - especially during that hour-and-a-half either side of high tide.
"If necessary, we will divert drivers on to other roads to allow them to continue their journeys safely, and sections of the Northwestern cycleway will most likely be underwater which will make walking and cycling hazardous."
The Transport Agency's SH16 Causeway Upgrade Project includes raising the section of the Northwestern Motorway 1.5 metres to prevent future flooding, Ms Musgrave said.
The king, or perigean, tides occur when the moon is either new or full and closest to the earth. Low pressure weather patterns and strong winds can also influence the height of the tide.