Last week torrential rain caused severe flooding in Southland, damaging houses and putting a strain on businesses in what should be their peak season.

Nearly 6000 people were evacuated from their homes across Southland, with Gore and Mataura hit the hardest.

Hundreds of tourists were also stranded in Fiordland after flooding damaged State Highway 94 and cut off access to the Milford area.

Gore says officials are keeping a close eye on the situation.

"We know that it's coming, we know it could potentially be significant, but there's uncertainty around that."

Emergency Management Southland was warning farmers in the region to be prepared.

"With soil moisture levels already very high following the flooding last week, farmers in particular need to be prepared and keep a watch on their local waterways and stock," it wrote on its Facebook page.

"We have the state of emergency for Southland still in place and the team at the emergency coordination centre are watching and preparing should the predicted rainfall arrive."

The MetService predicts the deep low will be felt most in Westland and Fiordland, though there was a chance there could be a "significant impact" in Southland and Otago, in addition to the west of the South Island.

There was a moderate chance of "warning amounts of rain" in Fiordland, Southland and Otago, MetService said, adding they had "high confidence" of heavy rain in Westland, with that expected to spread across to the headwaters of Canterbury lakes and rivers on Sunday and Monday.