The heaviest rain in two years brought 400mm to parts of the Milford Track, closing the walkway and confining trampers to huts.
The Arthur River is at record levels and high winds have struck the Mackinnon Pass. Both the Arthur and the Clinton River have flooded across the track.
No new walkers started the track on Tuesday and the 120 walkers already en route will stay another night in huts.
Although other tracks in the region are still open, DoC said trampers should watch for swollen rivers and other natural hazards.
MetService has issued a severe weather warning for heavy rain and gale winds in parts of the South Island and lower North Island on Wednesday.
It said the front should then move further north bringing severe northwest gales to Wellington and Wairarapa up to Hastings and across to Taranaki until early on Thursday.
Heavy rain's also expected about the Tararua Ranges and Mt Taranaki early on Thursday before easing.