The Department of Conservation says trampers walking on the Milford track will at times be wading through thigh-deep water, following more than 400 millimetres of rain on Monday.
Heavy rain in Fiordland forced DoC to close the track on New Year's Day forcing the 120 trampers on the walk to stay an extra night.
More than 400mm of rain fell on the western side of the 53.5km route on New Year's Eve, causing both the Arthur and Clinton Rivers to flood across the track.
Water levels rose above head height in some areas.
Milford track was reopened on Wednesday morning because river levels had dropped.
DoC spokesperson Annie Wallace says despite the reopening, people still need to take extreme care.
She says some of the walkers will be at least in knee deep water and up to 400 metres may be thigh deep.
Ms Wallace says there are some children on the track who may need to be carried some of the way.
Forty new trampers will begin their walk on Wednesday.
AAP reports 40 people who were booked to start the track on Tuesday will their hut fees refunded.
They will have to rebook to walk the track at some time in the future, or try to walk one of the other tracks, the Routeburn or the Kepler.
Popular routes are heavily booked at this time of year.
In March 2010, 120 trampers were airlifted from the track after a storm there. Twenty people were also taken off the Routeburn Track.