MetService has issued an orange rain warning for Fiordland from 5pm Monday until Wednesday morning.
Up to 250 mm of rain is expected - most of it on Tuesday - with as much as 300 to 350 mm falling between Doubtful Sound and George Sound.
Peaks rates of 15 to 25 mm/h expected, rising to 30 to 40 mm/h over Tuesday morning.
Meanwhile, Fiordland and Southland should brace for strong winds between 5pm Monday and 6am Tuesday, MetService said.
Stewart Island may also be affected by north to northwest winds, which may approach severe gale in exposed places.