"When it rains stormwater makes its way into the sewers in a variety of ways such as cracks in ageing pipes or gully traps being incorrectly hooked up into the wastewater system and so on.
"When the capacity of pipes is exceeded, a combination of wastewater and sewage overflows into the environment."
Pfahlert said the cost of fixing infrastructure issue could be "huge".
Auckland Council was spending $1.2 billion on its new Central Interceptor to separate wastewater and stormwater flows.
It was expected that will reduce the annual overflow volume to its harbours and waterways by 80 per cent.
"But it's far from just an Auckland problem. The NPR data revealed that 35 out of 41 authorities in the review report some level of sewage overflows caused by wet weather."
Fewer than half of the authorities in the NPR had reported design standards for preventing overflows and fewer than a quarter have standards for the frequency of overflows communities can expect.
"With local council long term plan consultations under way around the country, this is the time for communities to have the tough discussions about the level of protection we expect to afford our waterways and the price we're willing to pay for that protection."
The report comes as a new year-long investigation will take a closer look at the country's stormwater and wastewater systems, after an initial study found much of the infrastructure could be inundated by a threat it was never designed for.
Heaping pressure on around 24,000km of public wastewater networks, more than 3000 pump stations and 17,000km of stormwater channels could be sea levels, which are projected to rise up to a metre by the end of the century, and the likelihood of more frequent extreme rainfall events.
Many local water systems have been designed only to be used as secondary stormwater routes in extreme flooding.
But in the kind of weather that could come with climate change, sewage could gush into stormwater overflows, causing contamination problems like those which dogged the clean-up of flooded Edgecumbe last year.
In coastal areas especially, rising oceans and more frequent big storms could lead to sewage overflows, damaged and corroded pipes, liquefaction, and electrical failure at treatment plants.
The new study, supported by the Deep South National Science Challenge, will trawl through research to pinpoint the areas in the firing line.
That would mean assessing where impacts might be more likely to occur, or hit hardest, because of factors like ageing networks, vulnerability to flash-flooding, pressure from development, or rising groundwater.