MSC and WSNZ urge those in the West Coast, Tasman and South Westland to "postpone planned trips" in light of the severe weather warnings.
DoC's Golden Bay operations manager Dave Winterburn said "lower lying areas of the track are of great concern" due to high tides and rainfall.
"We haven't been able to check and assess the track yet as staff are committed to assisting Emergency Management."
DoC said it was too early to assess the state of the Heaphy Track and was aware of an incident Karamea River area on Wednesday morning.
Maritime New Zealand confirmed that a rescue helicopter was sent to the area to assist a stranded hiker who was flown to Nelson, shortly before midday.
Coastal tracks, river crossings and tidal swells add to challenging conditions for much of the South Island.
New Zealand saw 15 drownings over the Christmas period taking the total of 74 lives lost in the water according to WSNZ.
A moment to think about water safety could save your loved one's lives, says WSNZ chief executive Daniel Gerrard.
"Remember the water safety code. Be prepared, watch out for yourself and each other, be aware of the dangers and know your limits," he says.
In the connected areas affected by the weather system well into Otago, trampers are advised to avoid river crossings this weekend, with high waters predicted.
If you are planning a hike this weekend, check trail conditions and warnings via DoC alerts or the MSC Plan my Walk app.
Covid-19 in the community
Hikers' plans should also factor in the rise of Covid-19 in the community. With the spread of omicron over the long weekend, hikers should be prepared to isolate or return home at short notice.
Should you or one of your party contract Covid-19 your travel plans must not involve public transport, ferries or air travel. You may be required to test and isolate away from home, at your own cost.
