Threatened forest species may face a plague of predators if a bumper beech season leads to a surge in rodents, which then make meals of endangered birds and bats.
However at the same time, a study has shown booming native bird populations in urban reserves are likely to upset city dwellers with their songs and droppings.
The Department of Conservation (DOC) said beech trees were flowering heavily across the country following ideal climate conditions in the past two summers.
That will lead to large amounts of seed falling next autumn, providing abundant food for rats, stoats and mice.
DOC Director-General Lou Sanson said there were concerns that when the seed supply ran out in winter, rodents would prey on vulnerable species, like native birds, bats and snails.
Scientists would monitor beech forests for rodent numbers, he said, and pest control specialists would identify at-risk populations and prepare contingency plans for pest plagues next winter and beyond.
The prolific flowering could lead to the biggest seeding event in more than a decade, said DOC scientist Graeme Elliott.
A similar event in 2000 reduced mohua in Fiordland from several hundred to a dozen or so birds, and wiped out a population in the Marlborough Sounds.
"Birds like mohua/yellowhead, kakariki karaka/orange-fronted parakeet and whio/blue duck are particularly vulnerable, as well as other threatened species such as short-tailed bats and Powelliphanta snails," Dr Elliott said.
Meanwhile, pukeko, kaka and red-billed gulls are expected to boom in urban areas, testing people's tolerance for noise, fouling and nesting.
A study by Victoria University's Centre for Biodiversity and Restoration Ecology found those species consumed a wide variety of foods, leading to population growth.
The success of nature restoration projects in cities could also bring more forest or seaside-dwelling birds into cities.
Researcher Dr Wayne Linklater said large and dense populations could amplify problems "such as noise, fouling or nesting".
The study, co-authored by Master of Science graduate Kerry Charles, was published in the journal Wildlife Research.
Ms Charles said kaka were already causing contention in Wellington by damaging property, particularly trees.
"Our study suggests that there may be further problems caused by birds in New Zealand cities as our cities become more urbanised and populations of birds with broad diets grow," Ms Charles said.