When you swim over a patch of healthy, flourishing golden kelp in Port Phillip Bay, the fronds surge in the current and small fish dart in and out.

But the kelp forests in some of Melbourne’s best-loved marine sanctuaries have been nibbled bare by the soaring numbers of native purple sea urchins, which turn the reef into grim stretches of bare rock and algae-covered sand.

Now a group of conservation organisations – including The Nature Conservancy Australia and experts from the University of Melbourne, Deakin University and Parks Victoria – has launched a golden kelp restoration project to recover these habitats.

“We are at the point where if we don’t intervene ... we’ll continue to lose those important habitats,” said Scott Breschkin, The Nature Conservancy Australia’s oceans coordinator in Victoria.

“If you snorkel above an urchin barren it’s a confronting sight – bare rock, some coralline algae, devoid of all those marine plants you normally see on a thriving reef.”

Golden kelp, Ecklonia radiata, is a naturally occurring seaweed that grows in the cooler waters of southern Australia. The urchin problem in Port Phillip Bay is so widespread that more than 60 per cent of reefs is affected by urchin overgrazing.

This will be the first trial in Victoria to cultivate golden kelp at the microscopic level to plant onto reefs. It builds on similar work in Tasmania to select and grow heat-resistant varieties of critically endangered giant kelp to withstand rising ocean temperatures.

The project will focus on rocky reefs within and outside of marine protected areas, and will also involve culling of overabundant purple urchin populations. When urchins overgraze, they create rocky and sandy areas devoid of marine life, known as urchin “barrens”.