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Emergency Management Southland this afternoon warned of the risk of surface flooding ahead of heavy rain which was expected in the region overnight.
Emergency Management Southland community adviser Aly Curd said there is the potential for significant rain in isolated areas, particularly in the catchments east of Lumsden.
There is a severe weather warning in place as well as a severe thunderstorm watch, which could provide even heavier localised rain, she said.
"We can expect some surface flooding and will be monitoring the headwaters overnight and if we have any concerns we will notify those in the affected areas."
MetService said a series of troughs over the Tasman Sea would move eastwards across the country today and a deepening low was forecast to cross the lower South Island overnight tonight and Wednesday morning.
Rain was expected in many South Island places with the heaviest falls in Westland, Buller and Southland and heavy rain warnings were in place for these areas.
The warning for Southland is an upgrade from a heavy rain watch which was issued this morning, along with one for Clutha. MetService also issued severe thunderstorm watches for both areas.
The warning for Southland was in place from 6pm tonight until 10am tomorrow when 50mm to 70mm of rain was expected to accumulate, with peak intensities between 15mm to 25mm per hour.
MetService meteorologist Karl Loots said a band of heavy showers and thunderstorms was sitting offshore of the North Island's west coast early this morning and was about to move over land.
The entire North Island, bar the east coast, would see showers with a moderate risk of thunderstorms for the day.
Otago and Southland would see some scattered rain, clearing this morning, before some potential thunderstorms, showers and even downpours in the afternoon and evening.
Auckland is being hammered this morning by a massive thunder and lightning storm causing flights to be delayed and houses to shake.
All domestic flights have been delayed until further notice because of the lightning, travellers have been told.
Those who had just arrived were told there could be a delay getting their bags because there was a lightning warning for the airfield.
The storm was causing problems with the alarms in the terminal causing them to go off but travellers were being told to ignore them.
The heavy weather comes after several days of the same.
On Sunday parts of Hamilton saw flash flooding, causing homes to be evacuated and half a dozen becoming uninhabitable.
Then on Monday four people were injured after a lightning strike at Hamilton North School.
Loots said it had been a "very active" few days of thunderstorms.
Around midday today through the early afternoon the fronts will clear for periods of sunshine in the North Island, before showers returned in the west this evening.
Eastern parts of the country were in for a relatively fine day, with Napier in for a high of 27C and Canterbury 25C.
Some spots could see significant northwest winds, gradually increasing and getting close to gale, especially in Wellington.
These fronts would move over the country today, before another affected the far south tomorrow morning, bringing in some cooler weather.
"We have had this very strong, warm, humid northerly flow the past few days," Loots said.
"This will change around Wednesday when the wind will swing around to the southwest."
It is not all bad though, with a high pressure forming Thursday into Friday and Saturday, bringing some fine weather for most places at long last.
- additional reporting ODT Online