After record November rainfall, the water off Oamaru Harbour was visibly brown and turbid.
And although by mid-December, from the shore, the water looked clearer, the underlying turbidity was still having an effect on the birds' behaviour.
Oamaru Blue Penguin Colony research scientist Dr Philippa Agnew said, at the end of November, as fewer birds were coming ashore at night it could indicate that in the turbid water the little penguins needed to spend more time away from their nests foraging for food to bring home to hungry chicks waiting at the colony.
As Massey University comparative endocrinology professor John Cockrem was visiting Oamaru to get hands-on experience with tracking devices, Dr Agnew and Prof Cockrem sent out four birds equipped with GPS tracking devices to see whether the increased turbidity levels might have influenced where the birds were foraging as well.
''[Prof Cockrem] happened to arrive two weeks, three weeks, after we had a really unusual storm event,'' Dr Agnew said. ''So, the fact that we have managed to put some trackers on and see what the birds are doing in the aftermath of this unseasonably rough weather, adds to our understanding as well.
''The indication is that they might not go to where they normally forage.''
Further, chick weight was down at the colony, lower than in previous breeding seasons and lower than before the rough weather. Little penguin chicks were from 100g to 200g smaller than they should be.
It was earlier hoped that this would be a record-breaking breeding season for the little penguin colony, but at this stage the storm's effect was uncertain.
In 2015, a major winter storm had a significant effect on Oamaru little penguins - only 60% of the adult birds survived the year rather than the 86% average.
''This won't impact our long-term growth [but] it is concerning that the weather event has had a larger impact than we anticipated,'' Dr Agnew said.
''Let's face it, these little guys are really hardy and they are really resilient, so even though the likes of the 2015 storm - we saw a lot lower survival in that year - they will rebound. And generally, the fledging survival is lower than the adult survival, anyway. It's the adults that are the important ones in terms of population growth.''
However, Prof Cockrem, who originally came to Oamaru to test whether solar-powered tracking devices would be suitable for the world's smallest penguin - as the devices which were attached to a bird's back were suspected to be too big for the species - said the long-term data at the colony could allow scientists to understand the effect of a major weather event on the species.
''With climate change, of course, weather patterns that were unusual are going to become more common and so here the data from the penguins ... will provide an indication over the medium term of how these weather events are impacting on penguins.
''If an event, a poor breeding situation, starts to happen every five years instead of every 20 years, that will be shown here.
''And that will inform us about the vulnerability out into the future of penguins and further emphasise the need to do everything we can to protect little penguins nesting on the mainland, wherever they are.
''In any location where there are penguins nesting, we really don't know where they go out to sea and we don't know which areas are particularly important - it might be that most of the year birds go and feed in a particular area, but at one time of year they might feed in another area. That information is of value for our understanding of the biology of the bird. But it's really valuable in terms of conservation, determining which areas are important for penguins to feed in.''
