Niwa geologist Helen Neil said the survey showed that the gulf's bottom was "spectacularly flat" compared to Niwa's last survey - a map of the Cook Strait which showed dramatic canyons and the remnants of shipwrecks.
Most of the gulf was shallower than 50m and smooth-bottomed apart from small reefs and rocky pinnacles.
"At first pass you do think it's typically flat, but if you look at specific regions there's sand waves, rocky reefs, scour in the channels where currents speed up, which people living in this region who sail and swim and dive will find quite interesting."
The seafloor was mostly flat because 20,000 years ago the Waikato River flowed into what is now the Waitemata Harbour, before sea levels rose and drowned these plains.
"Think of the Hauraki lowlands today. That was what the Hauraki Gulf was like, it was above water, it had a large river meandering across it and depositing all the sands it was draining from Lake Taupo," said Dr Neil.
She said the survey was "a work in progress" and therefore had not picked up some of the gulf's mysteries, such as the wreck of the RMS Niagara, sunk by German mines in the gulf 70 years ago and now 120m down.
The images were generated by sending a fan of 500 simultaneous acoustic beams (or pings) from the research vessel Tangaroa. The shape and type of seafloor surface were then measured by the speed, angle, and the way in which each ping returned.
"If you think of dropping a tennis ball straight down onto a table it comes back up quickly, but if dropped to the floor it's slower. That's how these fans of beams work," said Dr Neil.
The most dramatic parts of the underwater landscape were the channels between islands, where squeezed corridors of water had scarred the sea bottom. The seafloor between Motuihe and Motutapu Islands had deep scour marks, pits of erosion and coarse, gravel-like sediment.
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