Search co-ordinator Sergeant Ian Martin, of Invercargill, said a body located near Teal Bay on Saturday was that of a 69-year-old woman.
Some debris from the boat was found on Sunday.
Her 65-year-old partner was still missing. Both are believed to be from Christchurch.
Sgt Martin said they intended to spend a couple of days at one of the huts beside the lake in Fiordland National Park and were in a small fibreglass boat on Friday.
Police were notified later that day that they were missing.
Sgt Martin said the shoreline of Lake Hauroko, along with the wider Wairauahiri River area, would be searched on Wednesday.
Maritime New Zealand investigators would be also be involved.
Once water levels recede and conditions became more favourable, the Police National Dive Squad would join the search, he said.
Sgt Martin appealed for boaties using the lake to contact Invercargill Police on (03) 211-0400 if they saw any debris.
Police said they would like to thank volunteers who have assisted with the search so far, including members of Southland LandSAR, the Volunteer Amateur Radio Emergency Communications Group, and the Fiordland Water Rescue Group.
