Of significance was the increase in black-billed gulls, she said.
Dr Crisp said they were worried because there weren't as many at the Ruamahanga River nesting site as in previous years, but then they turned up in good numbers at the lake.
"We were just happy to see that there were still good numbers of them."
"Black-billed gulls are in quite serious decline."
Predators, irrigation and nest disturbance are all common causes of decline.
The census also found the numbers of dabchicks, black shags, little black shags, little shags, and Caspian terns increased substantially.
Dr Crisp said the lake is quite a significant home for many birds, with more than 6000 individual birds being counted.
Canada geese dominated the census with more than a thousand counted.
"There are huge numbers of Canada geese because they multiply really quickly," said Dr Crisp.
The lake level was relatively high during the survey which meant unusually low counts for shorebird species like the pied stilts, banded dotterels and black-fronted dotterels.
Highlights of the survey included the four white herons, one little egret (a rare Australian vagrant) and one bittern spotted at the lagoon behind Willow Island.
A single pied shag was spotted swimming in the Tauherenikau Delta - the first pied shag recorded along the eastern shoreline since the survey started in 2011.
There were decreases in the numbers of South Island pied oystercatchers and spur-winged plovers.
The results compare average species counts from June 2011-2013 surveys with those from earlier surveys done from 1985-1994.