Napier residents are urged to limit the use of toilets, showers and washing machines to prevent contaminated stormwater flowing into Ahuriri estuary.
The district had 53.2mm of rain on Monday, with a further 34.7mm of rain expected to fall through to midnight.
A Napier City Council spokeswoman urged the public to only flush their toilet when necessary, and hold off using showers, dishwashers and washing machines to prevent stormwater overflowing into the Ahuriri estuary.
"If an emergency discharge is carried out, this should prevent wastewater backing up and overflowing into city streets and properties," she said.
"Toilets, showers, dishwashers and washing machines all drain into the city's wastewater network, which is also affected by infiltration of stormwater."
Heavy rainfall, thunderstorms and even hail is forecast to stay across the region until mid-week, with up to 130mm of rain expected to fall in some areas of Hawke's Bay.
By mid-afternoon on Monday, surface flooding was evident in several roads and highways in the region.
A Waka Kotahi NZ Transport Agency - Hawke's Bay and Gisborne spokeswoman encouraged drivers to switch on headlights, slow down, increase following distances and drive to the weather conditions in order to be prepared for unexpected hazards.
MetService meteorologist Rob Kerr says the broad low pressure system currently over the north island is expected to linger until it's pushed eastwards by a ridge of high pressure.
"From now through to later Wednesday, parts of the North Island will see heavy rain or showers, with thunderstorms and hail possible, while strong or gale south to southeast winds affect the lower North Island," he said.
Kerr said the main area of concern is the ranges of Hawke's Bay and southern Gisborne.
A Heavy Rain Warning is in place for those areas, with 100mm to 130mm of rain expected to accumulate about the ranges from Te Haroto southwards, with 70 to 100mm elsewhere.
The warning began at 10am on Monday and is in place until 11pm.
Peak intensities are expected from Monday afternoon when hourly rates could reach 25 to 40mm/hr in thunderstorms.
"This is a large amount of rain in a short period and isolated downpours could see totals exceed that range," Kerr added.
Hawke's Bay Civil Defence Emergency Management Group Manager Ian Macdonald warned that heavy rain can cause streams and rivers to rise rapidly, with surface flooding and slips also possible. Driving conditions may be hazardous.
"It's always good for anyone driving to take extra care on days like this and keep an eye on the weather forecast," he said.
"As little as 30cm of water can cause people to lose control of their vehicles, so the usual cautions apply: slow down, drive to the conditions and stay safe."
The northbound lane of State Highway 2, near Tangoio, was blocked on Monday morning after a logging truck slid into a roadside ditch.
Emergency services were called to the crash about 8.09am on Monday, but nobody was injured.
Surface flooding also caused the Mohaka Township Rd, Mohaka, to be closed at the Nakis Rd intersection on Monday afternoon.
NCC said Kennedy Rd, at the intersection of State Highway 2 and Downing Ave, was also closed from 4pm due to severe flooding.
Eastern District Police said surface flooding was causing multiple issues with vehicles 'breaking down' when driving through floodwater.
The police requested the public keep vehicle traffic to a minimum until the flooding eases.
A Fire and Emergency New Zealand spokesman said a tree had fallen onto a caravan in Bluff Hill, Napier, due to the weather at 2.32pm on Monday.
Kerr said a "further burst of heavy rain" may be expected in Hawke's Bay on Wednesday before the low pulls away.
Hastings District Council and Central Hawke's Bay District Council said they had not experienced any weather-related issues.