From 2019 to 2022, Oamaru’s Sumpter Wharf had the largest colony of Otago shags but this year nest numbers have dropped by more than 500.
Dr Chris Lalas has monitored the population of the birds since 1977 but could not explain the decline.
While it had not been proven, he suspected a decreased food supply might be the issue.
Water temperatures had increased around the colony, which would impact the marine wildlife that the birds fed on.
The water temperatures had been affected by a combination of climate change, La Nino weather patterns and other cycles.
There was not a single explanation for the weather but rather a culmination of factors.
Dr Lalas said other Otago shag colonies had been affected, with the two other large colonies, in Moeraki and the Otago Peninsula, recording two-thirds of previous years.
Last year, Oamaru had 719 nests, which Dr Lalas said was double the size of other colonies.
Sumpter Wharf was first used as a nesting site in 2014 and the population saw a steady increase until its peak in 2020 with 737 nests.
Despite the dramatic drop in nests, it was "certainly nothing to panic about".
The colony had "just hit a bad year".
He jokingly suggested the shags were doing it so they could laugh at scientists.
"They’re probably having a few beers and having a good laugh in the evening."
Arrow Koehler, PIJF cadet reporter