Parts of Great North Rd near Clark St reopened overnight with a single lane in each direction.
However, Auckland Transport said not all lanes on the large road would be open in time for the start of the morning rush hour despite floodwaters subsiding.
The transport organisation asked motorists to try avoid this area or use an alternative route where possible.
Engineers would be inspecting the flood-affected road this morning.
Traffic flow showed heavy use of nearby Margan Ave which was this morning being used to bypass the waterlogged intersection and New Lynn's main thoroughfare.
More than 320 properties were flooded in a matter of hours in yesterday's flash flood, 225 in West Auckland, with some inundated by waist-deep water.
Meanwhile, a number of roads across the Auckland region remain closed due to flooding and slips.
They include Tawa St in Oneroa on Waiheke Island, a section of Falls Rd in Warkworth and parts of Twilight Rd, East Coast Rd and McNicol Rd in the Clevedon area.
Lagoon Drive in Panmure is also down to one lane due to a slip.
Parts of Waikumete Cemetery were also flooded, with a stream overflowing.
It is not yet known whether any headstones were damaged.
A number of schools in the Kelston, Glen Eden, New Lynn, Green Bay and Titirangi areas were also affected by flash flooding.
Playhouse Early Learning Centre in Green Bay did not open today.
Despite the bad weather, most schools have indicated they are still open today.
Green Bay High School has asked its Year 13 students to stay home today, as nine classrooms have had to be closed off.
"We hope to have them back in commission by Tuesday,'' a notice on the school's Facebook page says.
Glen Eden Intermediate is also open after it was inundated during the weekend.
"The staffroom is a little worse for wear with a major leak in the roof, but the teachers will be able to tough it out.''
Just two school across the region gave children the day off class. The Ministry of Education said Mercer School was closed due to road closures and Karangahake School in Thames Coromandel was also closed.
In the South Island slips and flooding continue to block State Highway 1 south of Kaikoura.
The NZTA is advising motorists to use the Inland Route through Waiua to travel between Hundalee and Kaikoura.