NZME's Mark Mitchell has been told a manhole halfway up the stairs popped.
The water was ankle deep at the height of the situation and there was nothing anyone could do until the rain subsided, he said.
Flooding inside the Wellington Train Station today - not looking good!
Video: Eloise O'shea
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Posted by Wellington - LIVE on Thursday, 7 March 2019
There were also reports of manhole covers coming off on central-city roads, which presented a significant hazard, a council spokesman said.
The prospect of play in the Black Caps' second test against Bangladesh is not looking good.
Pools of water can be seen on the ground at the Basin Reserve.
MetService meteorologist Tui McInnes said at 11am there had been 32mm of rain, "which is a decent amount".
"The arrival of the front that brought the rain was very nicely timed to match exactly up with the morning commute rush.
"The first drops started falling at about quarter past, half past seven, and by about quarter to eight it was hosing down."
There is a heavy rain watch for Wellington until 6pm, but the main period of rain was falling right now.
Residents could expect the weather to ease gradually, with showers and grey skies throughout the day.
He encouraged people to use "common sense" in the wet weather, particularly while driving.
Severe weather warnings are also in place for Bay of Plenty and Gisborne.
The heaviest falls are expected in eastern Bay of Plenty between 9am today and 6am tomorrow, and in Gisborne north of the city from 1pm today until 9am tomorrow.
The heavy rain watch in Wellington, is also in place for the Marlborough Sounds and the Kaikoura Coast, with heavy falls expected until 6pm tonight.
MetService Meteorologist Tui McInnes said the front was currently aligned over Wellington and along the west coast of the North Island, up to Kaitaia.
Wainuiomata had recorded 84mm of rain at 4am this morning, "which is a pretty decent dumping", McInnes said.
"The rain is pushing through and at the moment the general plan as the front goes through is it will keep things fairly wet and then start to clear this evening," he said.
Dawson Falls on the slopes of Mt Taranaki has also had 108mm of rain in the past 12 hours.
Nelson airport recorded 26.2mm of rainfall up to 10am this morning - the most rain seen since October last year.
While most of the wet areas are unlikely to get thunderstorms, Northland, Auckland and northern Waikato could face some this afternoon, along with eastern Bay of Plenty and inland Gisborne tonight.
The rain is then forecast to move across the North Island on Saturday, bringing rain to Bay of Plenty and East Cape.
On Sunday, a ridge of high pressure should briefly bring more settled weather. On Monday, however, a moist north to northeast flow will bring rain to the west of the South Island, continuing into Tuesday.
National Manager Road Policing Superintendent Steve Greally urged motorists to take extra care on the roads today.
"Weather conditions are poor in many parts of the country with heavy rain and high winds. The roads are slippery, and police are urging people to drive to the conditions," he said.
If you're driving in the rain there are several things you can do to help keep yourself and others safe on our roads:
-If it's wet enough to put your wipers on, it makes sense to put your headlights on as well. Slow down.
-It helps you brake more gently and gives you enough time to react and retain full control of your vehicle.
-Move away from the vehicle in front to increase your stopping distance.
-Don't forget to buckle up!
