It was once famed for its gin-clear waters but today the waterways of the Norfolk and Suffolk Broads are more typically a murky greeny-brown.

Now a new “bio-manipulation” project aims to restore clear waters to Ranworth Broad and Barton Broad, paving the way for the return of osprey, common terns and rare aquatic plants currently thwarted by the murky depths.

Areas of both freshwater lakes equivalent to the size of 24 football pitches will be netted off, with populations of certain fish species reduced in each section during the £500,000 restoration project led by the Norfolk Wildlife Trust.

Conservationists believe that managing fish species that devour algae-eating zooplankton will “tip the balance” and permanently remove the excess algae that causes the turbid waters.

While the Broads’ terrestrial marshland and reedbeds are rich with unique wildlife, from swallowtail butterflies to Norfolk hawker dragonflies, conservationists liken its waterways to a forest where all the trees have been felled.

The historic cause of the Broads’ murky water has been untreated sewage and fertilisers from intensive agriculture washing into the rivers. This influx of nutrients has caused algae to thrive, which prevents light reaching the bottom of the lakes, causing aquatic plants to die off.

Predators such as pike can no longer hide among the plants, leading to unnaturally high populations of roach and bream. Roach feed on the zooplankton which would ordinarily eat algae, while bream stir up the silty bottoms of the waterways, sending nutrients back into the water and further boosting algal blooms.

“If you imagine a forest with lots of predators and prey and all of the sudden the trees are taken down – the predators have nowhere to hide up,” said Kevin Hart, the head of reserves for Norfolk Wildlife Trust. “Once you get the plants again, the fish species start to regulate themselves.”

Just as restoring wolves to a re-wilded landscape can create a “landscape of fear” and reduce grazing damage, so a “cascade” of positive effects will occur in the aquatic ecosystem, according to Hart. Predators including pike and osprey will reduce the impact of the grazers – zooplankton-feeding fish – by moving them around more.

The restoration attempt is possible because the nutrients that once poured into the Broads are now restricted thanks to the efforts of farmers, the Broads Authority, the Environment Agency and others. But although harmful phosphates have now fallen to levels that could sustain clear water, the algae retains a stranglehold.

Forty years ago, conservationists closed off one of the Broads’ freshwater lakes, Cockshoot Broad, from the main river system to restore its water. Cockshoot’s water is still clear, with rare aquatic plants, such as the holly-leaved naiad, thriving.

According to Hart, the switch from murky to clear water could happen within weeks of the new netted areas being built, with roach and bream being swept unharmed from these areas during the installation.

With funding from the Biffa award – created by landfill taxes – areas close to the banks of the Broads will also be enclosed, and their fish populations monitored and managed to encourage the development of more than 800 plant species that thrive on the water’s edge.

The project should benefit pike and water vole and could double the breeding population of common terns on Ranworth Broad, with new islands for their nests also being created.

When the waters clear in the enclosed area of Ranworth Broad, the trust hopes that it could trigger the clearing of all of Ranworth’s waters within a few years.

“The idea is to do enough to tip the whole balance of the Broad,” said Hart. “This isn’t against fish but about balancing the population of fish species. We need to do this to kick the current [algae-dominated] system over. Once we do that it will be sustainable and a much healthier system all round.”

Pamela Abbott, the chief executive of Norfolk Wildlife Trust, said: “Both Ranworth and Barton Broads are located in the midst of some of the finest terrestrial fen habitats anywhere in Europe. The biodiversity potential of the Broads is immense and this significant grant allows us to restore and reestablish aquatic plant life.”