A car and truck collided in floodwaters on State Highway 1 near Tawa heading towards the capital, causing traffic delays.
Police said the crash happened on a part of the motorway where there was significant flooding.
The Transport Agency said traffic was heavily congested after the collision.
The vehicles had been cleared away and all lanes were open, but the agency advised drivers to consider an alternative route or delay their journey where possible.
There were also warnings of surface flooding in other parts of Wellington, including on the Petone Esplanade, where one lane was covered in water early this morning.
MetService forecaster Tom Bell said the downpours had been concentrated in Tawa, which had about 20mm in a two-hour period this morning, and Khandallah, which had 15mm. Porirua and Lower Hutt each received about 7mm.
Rain would continue in Wellington today but was not expected to be heavy, he said.
Heavy rain is expected in the South Island.
A warning is in place for Westland south of Otira, where rainfall totals could reach 80-120mm in the ranges and 50-80mm nearer the coast.
There is a watch for heavy rain in Canterbury and North Otago, which could get 50mm today.