Rainfall would become heavier, with more chances of "extreme" intense rainfall events, due to more moisture being held in a warmer atmosphere.
Being next to the Cook Strait means coastal parts of Wellington such as Petone will be more affected by sea level rise, as well as inundation from storms, and coastal erosion.
Niwa chief scientist climate, atmosphere and hazards Dr Sam Dean said the report showed clear impacts, including on public health and agriculture.
But he said it wasn't about focusing on "doom and gloom", but presenting the options to deal with the problem.
"Reaching a long range target is hard, so I think the key for mitigation is changing our trajectory," Dean said.
"Just moving away, right now, from putting ever-increasing CO2 into the atmosphere.
"To start to embed those systems that allow us to slowly but surely reduce our CO2.
"In transport that might mean a shift to electric vehicles. People have choices themselves, in how they travel and work.
"I don't fear for the future, I think there are opportunities for us as a society that we can seize and make the most of."
Greater Wellington Regional Council chairman Chris Laidlaw said the report showed how important it was to take urgent action.
He said councils around the country wanted a framework from central government, to give them the legislative muscle to make the necessary changes.
"There is a huge groundswell around the country demanding more action.
"I get letters from people saying 'why are you not doing more?'"
Laidlaw said the situation for the Wairarapa was particularly worrying, with a likelihood of "severe" water shortages.
"There's this perception that New Zealand's contribution to this global effort is so small as to be unimportant, and therefore what's the point.
"The truth is that most of the developed world is doing better than we are. And in some cases, it's harder for them.
"So the excuse that we can't make any difference really doesn't stack up."
Laidlaw said it was important for individuals to also make what changes they could for their own lives, including taking more public transport, conserving water, and using less home heating.
KEY FACTS
• Temperatures in the Wellington region could rise between 3-4 degrees by 2090, and one degree by 2040.
• The number of days over 25C will almost quadruple for the Wairarapa, going from 24 days per year to 94 by 2090.
• It also quadruples for Wellington city, going from six per year to 26.
• Risk of drought will increase for Wairarapa, a key agricultural region.
• Winter will get wetter and spring drier. When rain does fall it will be heavier and more likely to be an "extreme event".
• Autumn will be the season to warm the most.
• Agriculture will be impacted by droughts, as well as increased heat stress for cattle, and overseas pests finding it easier to get established.
• Health impacts include more mosquito-carried diseases and premature deaths from heatwaves.
