They're small, cute and lure about 130,000 visitors to their island every year.

But the little penguin population that gives WA's Penguin Island its name is in danger on several fronts.

The 12-hectare island is just 600 metres off the coast of Rockingham, in Perth's south, and home to about 1000 little penguins, the largest colony that far west in the world.

Penguin Island is just 600 metres off the Rockingham coast. ( ABC News: West Matteeussen )

But changing weather conditions and rising ocean temperatures are playing havoc with their breeding cycles.

Belinda Cannell has been monitoring the penguins on the island for almost 25 years and has watched the population halve in the past decade.

"We see a lot of variation in the timing and the success of breeding, but … the breeding success has been much lower than in previous years," Dr Cannell said.

A destructive marine heatwave

In 2011, a marine heatwave caused a current of water 5 degrees Celsius warmer than average to travel down the west coast of Australia.

It culled several species of small fish that make up the little penguin's diet.

The penguin population on the island is closely monitored. ( ABC News: Pamela Medlen )

"Since then those sea surface temperatures have been above average in most years and particularly in the winter months, so this is what we're thinking is really impacting the penguins' availability to get food close by and therefore to breed," Dr Cannell said.

"Their main resource was whitebait — they also eat pilchard and anchovy and blue spratt — but with the marine heatwave, we saw an increase in the tropical sardine in their diet which we had never been seen before."

She said the penguins needed to travel further and further from the island to find food, sometimes hundreds of kilometres down the coast as far as Busselton or Margaret River.

"That's a long way for a little penguin to go and they're away for 15 days sometimes. That means the partner's sitting on the eggs and getting to a point where they have to abandon the eggs because they're just too hungry," she said.

"Then once the chicks have hatched they have to stay closer to the island, … and if they haven't got enough food they either stay out for longer or they come back and there's less food to feed the chicks."

Dr Cannell says warmer sea temperatures decrease food availability for penguins. ( ABC News: Pamela Medlen )

Department of Biodiversity, Conservation and Attractions marine park coordinator Melissa Evans said climate change had brought more frequent and severe storms, which caused erosion.

"That means that these little cliffs form, but the penguins can't get up the cliffs to their nest boxes or their nesting sites because they can't walk up these vertical cliffs, so that means they can't get back to swap with their partner or feed their chicks," Dr Cannell said.

Hotter West Australian summers were also killing penguins, she said, and one of her PhD students had been experimenting with different ways of protecting the penguin nesting boxes from heat.

Some of the nesting boxes had been painted with heat reflective paint, others had been covered in a shade cloth tent or had holes drilled into them and been orientated to aid airflow.

Human impact on penguins

Dr Cannell said about 25 per cent of penguin deaths were due to boat injuries.

"We can't do much about climate change and we can't change the fish that are available in the sea, but what we can do is reduce any other impact we have control over — managing people on the island, trying to have nest boxes that are cooler for them," she said.

"Reducing impacts in the water, try and make people aware the penguins are out there and their boating, they need to be slowing down and be aware the penguins are often just a metre under the surface of the water and they're difficult to see.

"Taking away your fishing line, don't leave your plastic pollution around because the penguins get entangled in that, and making sure that any coastal development we have is sensitive to where the penguins are."

Penguins have little resilience when it comes to environmental changes, Dr Cannell says. ( ABC News: Pamela Medlen )

Ms Evans said the DCBA was working with the City of Rockingham to make any events on the mainland foreshore plastic-free.

"Because it's a popular tourist location as well, it's important for us to try to balance people being able to use the island for recreation, but also conserving the environment so the wildlife is still able to use it successfully," Ms Evans said.

"There's extensive boardwalks around the island now so that gives people access to all of the great lookout spots and all the fantastic beaches, but it also keeps them up off the areas that are used by penguins."

Funding to continue her research is running out, but Dr Cannell is still collecting samples of faeces and downy feathers in the hope they can one day be analysed to find out whether the penguins are adapting to changing food sources and what can be done to protect both the fish and the penguin colony.

"At the moment it's not looking good, the viability of this population is decreasing and the population estimates have halved since I did an estimate in 2007, so that's not a good sign," she said.

"We need to try to do everything that we can to improve the breeding success of these birds and have this colony here for another 100, 200, 300 years to come."