She said at 5am the rain was so bad, Aro St resembled a river and she had never seen such severe flooding in the street.
Ms Cross said when delivery drivers pulled into the carpark outside the bakery early this morning a "wave" of water came into the shop.
The Fire Service was called to 30 flooding incidents in just two hours this morning. Most of these cases were in central Wellington, a spokeswoman said.
The flooding also caused problems on roads near the Basin Reserve.
Police said officers were at the scene of surface flooding on Roxburgh St and Marjoribanks St.
MetService said an area of low pressure moving over New Zealand yesterday and early today caused heavy rain and strong winds.
"All the main centres have seen a decent dumping of rain with parts of Wellington receiving over 50mm since midnight Sunday. Northerly wind gusts also reached over 100 km/h around Auckland's harbours on Monday night," Mr Glassey said.
As the low scuttled away, it would leave behind a cooler southwest airflow with showers still affecting many areas, MetService said.
The forecasters expected these southwesterly winds to strengthen tomorrow, with the strongest gusts expected around the southern coast of the South Island between Bluff and the Otago Peninsula.
MetService issued a severe weather watch for exposed parts of Southland, Otago and Banks Peninsula, as well as Hawkes Bay and Wairarapa between Masterton and Napier.
Some cold and frosty mornings were expected across the central South Island this week.
Temperatures in the North Island's central plateau were also likely to plummet this week and MetService expected some chilly nights there this weekend.
But MetService said showers should disappear from most of New Zealand later this week as a high pressure system moved in from the Tasman Sea.