Dr McLeod (30), undertaking postdoctoral research at the University of Otago, was presented with the award and the MacDiarmid medal by Research, Science and Technology Minister Pete Hodgson at a function in Auckland.
She also won the "understanding planet earth category" and received $10,000 and a trip to an international science event.
"It's really exciting. Unbelievable," Dr McLeod said.
Fellow University of Otago researcher Ursula Ellenberg won the "adding value to nature category" for her work showing yellow-eyed penguins were being loved to death by well-meaning visitors.
"I'm flabbergasted," Ms Ellenberg said.
Dr McLeod, who became engaged to be married last week, said the award was an acknowledgement of her research and would hopefully help attract funding for future work.
The research she presented was a study of the diet of primitive, scavenging hagfish, which live up to 400m below sea level in New Zealand fiords and ooze slime when annoyed.
"When you pull up the traps, there is this horrible, stinking snot everywhere. No-one ever wanted to work with me, but I suppose it's paying off now."
She discovered the hagfish obtained up to half their nutritional energy from coastal forest logs and leaves, which composted on the sea floor.
From there she developed chemistry tools that revealed energy transfer from the forest to the sea.
Her work will also feed into climate change research in the Antarctic, where a team of scientists will soon be diving beneath the ice and using Ms McLeod's techniques to learn more about marine food webs and the likely impact of warmer temperatures on ocean life.
"You're like a detective, and I like that. I'm continually surprised by what we are finding. It keeps you on your game," Dr McLeod said.
Ms Ellenberg (35), who is writing her PhD, said the category win was important as it showed her work had a purpose.
She studied the yellow-eyed penguin colony at Sandfly Bay, showing the birds did not breed as well as those in more remote sites - a result of stress caused by frequent disturbance by thousands of visitors.
Her findings, obtained by using hidden surveillance cameras and microphones embedded in dummy eggs to observe the birds, showed the birds to be one of the shyest penguin species in the world.
As a result of disturbance, the birds were more likely to abandon their nests and chick feeding might be disrupted, leading to reduced breeding success and lighter fledglings.
She received $5000 for her category win.
