Rising sea levels could reduce the availability of freshwater in some parts of the country, the Parliamentary Commissioner for the Environment says.
Jan Wright's latest report said it was certain the sea level was rising and would continue to do so.
Salt water intrusion was already causing serious problems for some of New Zealand's Pacific neighbours, she said.
The problem occurs when seawater moves into coastal acquifers.
In New Zealand most groundwater is taken from these acquifers, and in many parts of the country groundwater is a key source of water for drinking, industry and agriculture.
The Waiwhetu Aquifer in Wellington was particularly vulnerable to saltwater contamination.
The acquifer supplies more than a third of the capital's water demand and sea level rise was expected to reduce the amount of freshwater that could be taken from it.
"It doesn't seem to be quite such a problem around New Zealand from what we can see but I'm aware that in Wellington, the Waiwhetu Aquifer, which supplies I think 30 or 40 percent of Wellington's water, they do have to monitor that quite closely for saline intrusion - so it's something that certainly needs an eye kept on it."
Greenpeace New Zealand's executive director Russel Norman said New Zealand would start experiencing salt water contaminating freshwater, just like the Pacific Islands experience.
It was critically important that the country cuts its greenhouse gas emissions.
"This is where we in New Zealand are going to start to experience what those in the Pacific are already experiencing where with rising sea level you're getting the salt water invasion into the fresh water aquifers and that's having a dramatic effect across the Pacific already, and as the sea level rises we'll start to feel it in New Zealand as well.
Issues with coastal groundwater were expected to become more significant as the sea rises, Dr Wright said.
In some parts of the country the water table was not far below the ground and was connected to the sea, and as the sea rises the water table will follow suit.
High groundwater causes boggy ground and surface flooding as well as damage to infrastructure and buildings.
A rising water table would lead to surface ponding in some places and more extensive flooding after heavy rain, she said.
It would also damage roads, pipes, and cables, as well as the foundations of buildings.