Sewage has seeped into Wellington Harbour and south coast in the wake of a huge downpour on Friday.
Heavy rain that fell on much of the country was welcomed by farmers but disrupted major events in Auckland, Tauranga and Christchurch.
Wellington City Council has issued a pollution alert for the city's harbour, Lyall Bay and Moa Point, saying swimmers and other recreational users must stay out of the water as heavily diluted sewage was discharged down the long outfall.
The council is working with Regional Public Health over the issue, and was testing water quality over the weekend.
Untreated sewage was forced onto Courtenay Place in the central city by a blocked drain during the rainfall on Friday. A blocked sump caused knee-high flooding at one end of Lambton Quay.
Heavy rain affected the national kapa haka competition, a garden festival opening and a graduation parade.
The Fire Service says it had a busy afternoon in the northern region responding to weather-related callouts from the slow-moving front.
Paul Radden of the Fire Service's Northern Communications office says the 40 callouts ranged from surface flooding to roofs being lifted and fallen trees.
He says the callouts were mostly from the Auckland and Tauranga areas.
In Auckland rain forced the cancellation of a Queen St graduation parade for 1200 Auckland University of Technology students.
In Tauranga all Friday's performances of the national kapa haka competitions were postponed.
Slips were reported on State Highway 2 on the Wairarapa side of the Rimutaka Hill on Friday and in the Manawatu Gorge.
In Christchurch the opening ceremony of Christchurch's Festival of Flowers, which was to take place in Cathedral Square, was washed out.
But the month-long festival itself will go ahead over the weekend and the opening ceremony has been rescheduled for Thursday.
The rain also appears to have been behind a pile-up involving two cars and a bus at a busy Christchurch intersection.
Farmers are welcoming the rain, with Waikato Federated Farmers president Stew Wadey saying his members are extremely happy with it, especially as at this time last year they were facing a major drought.
It has also been welcomed by Whangarei farmer Denis Anderson, who says parts of Northland have had little rain since January.
MetService says the next few days are looking brighter.