Last month was the 11th warmest July on record, Niwa says.
Some parts of the country also had "well above normal" levels of rain leading to significant flooding, while others struggled through water shortage.
Niwa has released its climate summary for July 2020, showing the month was mild and near average for most parts of New Zealand.
But Northland suffered amid a once-in-500-year storm as Auckland battled to fill its dams.
Niwa's report showed Northland, western Otago, and inland Southland all had rainfall above the normal rate for that time of year.
It said overall rainfall was more than 149 per cent of the normal rate, but for other parts of the country it was less than 50 per cent of the usual rainfall.
"Most of Northland's rainfall occurred during the middle of the month, when a low-pressure system delivered very moist subtropical air to the region," the report said.
The mammoth storm flooded shops and forced residents to evacuate their homes, with 220mm of rain dumped on Whangārei.
The heavy falls caused slips and landslides that closed roads and limited water supplies.
Meteorologist Alwyn Bakker said the intense storm had been created by the unusual interaction between two low-pressure zones in a manner that caused a direct hit on Northland.
"We've done some calculations over here in MetService," Bakker said of the storm.
"And 220mm for Whangārei has what we call a greater-than-500-year return period.
"What that means is we see this kind of thing once in every 500 years."
The severe flooding followed weeks of water shortages, with Aucklanders instructed to restrict their water usage.
Residents were told to limit showers to four minutes and not use outdoor hoses.
The measures were the first of a four-stage alert system of increased restrictions to try to avert a worst-case scenario of turning off taps and making people line up for water at hydrants.
Auckland was not the only part of the country experiencing a dry July, with Timaru recording just 5mm of rain - 10 per cent of the average.
Meanwhile temperatures around the country were mild or near average. The nationwide average temperature was 8.6C, 0.8C above average. This made it the 11th warmest July since Niwa's seven station temperature series began in 1909.
"It has now been 42 consecutive months since New Zealand's nationwide average temperature was below average," the report said.
"Of the six main centres in July 2020, Auckland was the warmest, Wellington was driest and sunniest, Hamilton was the wettest, Christchurch was the coldest, and Dunedin was the least sunny."
• The highest temperature was 20C, observed at Whangarei on July 16 and Kaitaia on July 18.
• The lowest temperature was -8.9°C, observed at Tara Hills (Omarama) on July 16 and Middlemarch on July 18.
• The highest one-day rainfall was 262mm, recorded at Kaikohe on July 17.
• The highest wind gust was 191km/h, observed at Cape Turnagain on July 23.
• Of the available, regularly reporting sunshine observation sites, the sunniest four areas in 2020 so far are Bay of Plenty (1583 hours), Greater Nelson (1529), Taranaki (1520 hours) and Marlborough (1456 hours).