The funding package also includes $421,000 to extend Rural Assistance Payments for struggling farmers and $2m to support the rural sector across the North Island, parts of the South Island and the Chathams.
The new money is on top of the $2m granted by the Provincial Growth Fund to set up emergency water supplies in Kaikohe and Kaitaia.
Dairy farmer Will Tye told Ardern the season had been tough but farmers were "a resilient bunch". He was down about 10,000kg in milk solids but his biggest problem was having to buy in extra feed.
He said the drought was comparable to one he'd experienced on the Hauraki Plains in 2008 but long-time locals told him it was the worst they had seen.
"There's a few things coming at dairy farmers at the moment, and drought adds to the stress ... we could do with a few more wins."
Later, during a visit to Kaitaia's treatment plant, Ardern wouldn't be drawn on whether successive councils had dropped the ball on town water supplies.
The drought came on the back of several dry years in Northland, compounding current problems, she said.
In such extreme conditions it was not unreasonable for central government to step in and support the work of councils.
"Everyone accepts we are in an environment now where we are experiencing more extreme weather events and we have to plan for longer, drier summers and less rain in winter. This is not going to be an isolated event."
Ardern praised Northlanders' "amazing efforts" to reduce water use but warned that reductions would have to continue even if rain fell in coming days.
It would take a lot of sustained rain to put Northland back into a good position, she said.
Civil Defence Minister Peeni Henare said the extra $3m was targeted primarily for water supplies and treatment, as well as support for the rural sector. He would work closely with councils to make sure the money went exactly where it was needed.
"We hope this package not only relieves but also allows us to look forward to the future to see how we might mitigate these factors in the future."
Northland was particularly vulnerable in droughts due to high numbers of people relying on rainwater tanks and significant areas of deprivation.
Carter thanked the MPs for their support, saying the teamwork between central and local government, iwi and the community in coming up with solutions had made him proud.
"The community has stepped up. While there was some anxiety and anger two or three weeks ago, that is to a large extent gone and people are now working positively together."
