Wet weather can be expected in Christchurch and Dunedin, with heavy falls for both tomorrow.
As an active front moved across the island MetService said bursts of heavy rain could exceed 70mm in 12 hours in central and lower regions, with the possibility of localised flooding in Bay of Plenty and in headwaters of the Whanganui River.
MetService duty forecaster Tom Adams said winds accompanying thunderstorms could gust up to 90km/h.
"What's happening is there's a pretty active front crossing the island with a low centre. When that happens it can take time to get across, leading to heavy rainfall."
The wild weather kept people awake in Northland, where about 700 lightning strikes
were recorded offshore from the region in the early hours of Monday morning. Another 35 struck directly over land.
MetService meteorologist Lisa Murray said many of the strikes were cloud-to-cloud and while people would not have seen these, "they certainly would have heard the thunder associated with them".
The thunder and lightning was accompanied by a deluge, with Whangarei getting 20.6mm of rain between 3am and 4am on Monday, and 46.4mm between midnight and 10am.
Kerikeri experienced a similar downpour, with 21.4mm between 2am and 4am and overnight rainfall of 39.6mm.
Others also felt the force of the storm.
There were flashes of lightning in the Bay of Plenty and off the coast of Taranaki, as well as surface flooding in Rotorua.
More than 34mm of rain fell over 12 hours, causing surface flooding in Rotorua.
Relief is on the way in Rotorua, with temperatures and sunny breaks midweek before rain returns on Thursday and Friday.
Showers are possible across the region today, but Northlanders could also look forward to a forecast sunny day tomorrow with temperatures in the early to mid 20s.
Auckland: High of 18 degrees, morning showers then fine
Whangarei: High of 19 degrees, morning showers then fine
Tauranga: High of 22 degrees, fine with a chance of a morning shower
Wellington: High of 18 degrees, morning showers followed by fine spells
