Police said they were looking into what caused the tragedy.
It brings the death toll of people who have died in the harbour in a week to five.
Last weekend, two people died in water incidents on the Manukau Harbour in Auckland's first weekend of relaxed Covid alert level restrictions.
Water Safety NZ reminded Kiwis, particularly Aucklanders stuck in many weeks of lockdown, to check their gear and their own physical fitness before getting into their favourite water-based activities.
Police, Coastguard, and Airport Fire and Rescue were first involved in the search for a missing diver off the coast of Cornwallis Beach in West Auckland last Saturday.
Police confirmed they were notified around 8.25am of a missing diver.
The Westpac Rescue Helicopter and the Police eagle chopper were used to help the find man, who was located about 10am.
Police were still making inquiries into his death but it had been referred to the coroner, however a man who witnessed the search said the current and swells were very strong on Saturday.
"We felt like the water was tapu," said Victor, who only wished to give his first name.
On Sunday, emergency services were called to the Manukau Harbour to reports of a kayaker in difficulty off the coast of Hillsborough about 2.40pm.
A body was found and winched from the water.
The person's kayak was also recovered and police inquiries were continuing.
Water Safety chief executive Daniel Gerrand said he was also aware of a rock fisherman who was rescued at Bethells Beach on Friday after being swept off the rocks.
Fortunately the fisherman was wearing a lifejacket but it still required help from the rescue chopper and surf lifesavers from Bethells.
Aucklanders have been cooped up at home and were simply out of practice with their favourite activities.
"We haven't been out paddling, we haven't been out diving. There's equipment issues. We had a lot of diving fatalities last year and some of the feedback and insights was that the gear wasn't fit for purpose," Gerrand said.
"We've had such along time and people might normally have had their gear serviced by now and it's just that 'oh, she'll be right mentality' and heading out again and testing it.
"I think fitness has to be an issue, too. We've just not been doing these activities."