Another band of heavy rain is heading across the South Island and is expected to soak Canterbury and Otago overnight Monday.
The rain is not expected to ease until Wednesday morning.
MetService has issued a severe weather warning and says the downpour is likely to cause more flooding because the ground is already saturated from Monday's rain.
It says rivers may rise rapidly and more roads could be closed by water and slips.
People are advised to avoid driving where possible and use extreme care in flooded areas.
Meanwhile, Canterbury Fire Service says it is being kept busy responding to flooding-related calls.
The Fire Service is asking motorists to slow down because some drivers are speeding through flooded areas, creating surges that inundate nearby properties.
Shift commander Riwai Grace says so far they have received more than 75 flooding-related calls.
Upgraded storm water drains prevented worse flooding: council
Christchurch City Council says Monday's flooding would have been much worse had it not been for post-earthquake upgrades to the storm water system.
Flooding has been widespread across much of the city after both the Avon and Heathcote rivers burst their banks, and a number of smaller tributary streams also spilled over roads.
The water is receding but maintenance crews are remaining on standby overnight Monday with another high tide due around 2 am on Wednesday morning.
After a big day, council and civil defence staff are no longer expecting any major problems.
But Christchurch Council transport and greenspace manager Alan Beuzenberg says road closures still remain in place.
Mr Beuzenberg says the newly-upgraded storm water system has helped reduce damage.
In neighbouring Mairehau, it is a different story with knee-deep water flooding streets and nearby homes.
Some people blame silt from liquefaction that has built up stopping stormwater drains working effectively.
Mark McLean who lives in Thornton Street has spent much of the day trying to slow traffic down as vehicles negotiate his flooded street.
He says while he hasn't had to leave his house, he is expecting water to start seeping through his carpet overnight.
The wider Canterbury district has been hit just as hard, forcing Selwyn district council to close some roads.
It is warning that water races which feed irrigation systems from Hororata to Dunsandel are overflowing and people should take care near these.
Tai Tapu resident Sonya Cookson, who runs a preschool and grew up in the area, says she hasn't seen so much flooding since she was child.
And stormwater drains have overflowed into the sewerage systems so people are being asked to avoid flushing their toilets where possible.
Contractors will remain in Tai Tapu overnight monitoring the situation.
Near Akaroa, a water tanker will be set up in Old French Road off Takamatua Bay after the water supply ran out because of floods and a slip.
MetService records 60mm
MetService has recorded more than 60 millimetres of rain in the city's Botanic Gardens in 24 hours, with 100 millimetres falling on Banks Peninsula.
Several houses were flooded in Sumner and Lyttelton on Sunday night, and River Road, which runs alongside the Avon River and was severely damaged during the February 2011 quake, is flooded in many places.
The Fire Service attended 39 calls from people with flooded homes or properties.
Contractors met with the Christchurch City Council on Monday morning to brief city leaders on the flooding.
Motorists in Canterbury are being urged to drive with extreme care, as flooding has blocked some roads in the region and made others hazardous.
Christchurch City Council says slips and debris have fallen onto roads near Banks Peninsula, with the road between Little River and Christchurch blocked. Some roads are also closed in Lyttelton.
The council's civil defence manager, Murray Sinclair, says that while the forecast is for the rain to ease on Monday evening, more heavy rain is predicted for Tuesday.
He says staff have been preparing for more problems at high tide in areas such as St Albans, where there has already been a lot of flooding
Selwyn district roads hit
Heavy rain has taken its toll on roads in the Selwyn district, with its council urging people to stay at home or find alternative routes.
A council spokesperson says the Malvern Hills Road at the Waianiwaniwa Road end and all fords have been closed as a precautionary measure.
The spokesperson says Leeston Road and State Highway 1 bridges over the Selwyn River are open and likely to remain so.
Council staff and contractors are out around the district on Monday monitoring road conditions and signposting flooding.