Department of Conservation kiwi ranger Tim Raemaekers hopes at least one chick survives from the nests he monitors there.
Shy Lake is so remote it can only be accessed by helicopter, weather permitting, so there is no pest control.
So far, every chick from every nest monitored by Mr Raemaekers in the past three breeding seasons has been killed by stoats.
"It is year after year, all these adults trying really hard and just getting nowhere," he said.
In April 2017 Mr Raemaekers and his team started a five-year project at Shy Lake to study the survival rates of Southern Fiordland tokoeka chicks before and after an aerial drop of 1080 poison baits.
For the past three autumns, the team has tramped over Sky Lake's rugged hillsides "recruiting" adult kiwis to their project, capturing them and attaching transmitters to their legs.
In late winter and early spring, the team return to track those kiwis to their nests, where they have positioned trail cameras to film any movement around the entrances.
Once the chicks are old enough to be handled, and leave the nest at night on their own to feed or explore, they also get a transmitter. However, the team sometimes does not get there in time.
Some chicks died of natural causes last season, but tracking the transmitter to the carcass gave the team "definitive proof" the others were killed by a stoat, Mr Raemaekers said.
He explained that spending three consecutive years in Fiordland, finding the remains of one chick after another, was starting to wear him down after several years working on the successful kakapo breeding programme on Codfish Island.
"The kakapo were almost the opposite in that they were in really dire straits and had hardly any birds but now they are increasing in percentage terms quite fast.
"This project is at the other end of the spectrum; there are still a lot of adult kiwi in Fiordland but their numbers are decreasing because they cannot get their chicks through in areas where there is no pest control and eventually they are going to go down the gurgler. "
Shy Lake is home to many stoats but has surprisingly low rodent numbers. However, that was set to change
on the back of a mega mast leaving many more seeds on the ground.
The Department of Conservation has planned to drop 1080 over 40,000ha of the peninsulas north and south of Wet Jacket Arm, including the Shy Lake study site, next March when the rat population should have peaked.Stoats do not eat the toxin pellets - but they do eat rodents.
"Timing our drop for autumn is also designed to slow down reinvasion, as it will be after the peak period of stoat dispersal, when the juveniles leave their mothers in early summer and start running around all over the place."
After seeing first-hand the carnage stoats have inflicted on the tokoeka, Raemaekers said the drop could not come soon enough.
New technologies and genetic tools for pest eradication are being developed.
Even so, University of Otago AgResearch Chair in Reproduction and Genomics Professor Neil Gemmell said there was still no "silver bullet" for New Zealand's pest problem.
At a recent Royal Society of New Zealand Wanaka branch talk "Genetic Tools for Pest Eradication" Prof Gemmell acknowledged ongoing public discussion about the appropriateness of using 1080, nothing that "there is quite a vocal group that says it is dangerous".
"I don't agree," he said.
"It (1080 poison) works, it is our best tool. Would we like better tools in our tool box? Hell yeah! Could gene drives or gene editing be one of them? Maybe."
Prof Gemmell said using genetic control technologies or gene drives to achieve the goal of being predator-free by 2050 will only happen if it is "acceptable to the public".
Other scientists were developing engineered rats and if they were successful "we would easily be able to capitalise on their science", he said.
Stoats were a pest only in New Zealand and the Orkney Islands. As far has he knew, no-one was researching genetically modified stoats - although scientists had made a genetically modified ferret.
New Zealand, having lost 69 out of 245 bird species, is second only to Hawaii in bird extinction. Hawaii introduced tree snakes, carnivorous snails and avian malaria.
There was an optimistic prediction predators might be removed from an area as large as the South Island using traditional predator control, such as trapping and 1080 poison bait drops, by 2050.
"But wouldn't it be nicer if we could do it faster and cheaper."