Bay of Plenty residents are counting the cost of a torrential downpour in the early hours of the morning causing major flooding.

Torrential rain in the early hours of this morning caused significant flash flooding across the Mount Maunganui and Papamoa areas with the wet weather set to continue for the rest of the day.

Serious Straw Hats Mount Maunganui owners start the clean up after the overnight downpour.

Metservice forecaster Phillipa Murdoch says a serious amount of rain has fallen across the region overnight with the chance of thunderstorms expected this afternoon.

Tauranga Airport recorded the most rain from Metservice radars with 112 millimetres falling since 8pm last night while the Kaimai Ranges has recorded 43.6 millimetres.

The rain was concentrated on the Mount Maunganui and Papamoa areas with flooding submerging cars and parts of houses.

Residents are not in the clear yet with Metservice predicting thunderstorms and heavy downpours for the rest of the day.

Tauranga Harbour Bridge has reopened fully after being reduced to one lane while the State Highway 2 and Domain Road roundabout is open again after flooding.

Tauranga police sergeant Steve Hindmarsh says the water is beginning to subside and a number of drains which were causing the road blockages have been cleared.

Serious Straw Hats Mount Maunganui owner Morely Sutherland was first alerted to the flooding in the store by the owner of neighbouring Cole's Butchery.

'The butcher opens at 5.30 so he rang everyone up. There was quite a lot of our stock on the floor and it's all soaked.”

Morley is counting the cost of thousands of dollars' worth of damage after the heavy downpour came through the back of the store and out the front door.

'It was an incredible amount of rain. It was like a river through the shop.

'It will be a big day cleaning up.”

Oceanview Road resident Melissa Glover was woken up by firefighters who were outside attending to the torrential downpour.

'We heard the rain early this morning and just thought she'll be right.

'Next thing the doorbell is ringing for about 10 minutes and it was the fire guys waking us up.”

She says they went outside to find firefighters siphoning water out and everything floating around in the garage.

Tauranga City Council is advising residents to stay out of the Tauranga Harbour after some untreated waste water may have been discharged in to the harbour following a wastewater overflow at the Nikau Street Pump Station and the Waikareao Estuary.

They say tanker trucks are dealing with the issue.