On Sydney Harbour's pristine waters, there is no shortage of lavish yachts, eye-wateringly expensive catamarans and giant cruise ships.

But in some pockets is a hidden problem: Derelict vessels being left to rot, collapsing structures, crumbling jetties and their debris littering the waterway.

Stuart King first laid eyes on an abandoned boat in the harbour more than a decade ago.

"I was blissfully unaware because I was just enjoying the harbour, having a great time on the boat," the avid Sydney sailor said.

"I had a closer look at it, I thought, 'Wow, man, that's just ridiculous. How long has that been here?'"

Since that time, Mr King has come across dozens of dilapidated private and commercial vessels while sailing around in his rigid inflatable boat.

There are boats with broken railings, snapped masts, shattered windows, weathered seats, grime and holes tucked away in bays across the harbour.

In an audit conducted along eastern Sydney earlier this year, Mr King counted more than 80 unusable vessels.

"When I went out on that day-and-a-half and photographed over 80 vessels, east of the bridge, that were not capable of making a voyage, then why aren't Transport for New South Wales boating and safety officers doing that?" he said.

There are plans for another audit in the waterways to the west, where Mr King believes he'll document "an equal number, if not more, of similar, poor condition vessels that are derelict, unloved, unwarranted and should be gone".

"The owners should deal with them, not leave them to the taxpayer."

'It's a war on wrecks and ruins'

Mr King is co-chair of a campaign called Save our Sydney Harbour, who are pushing the NSW government to clean up the harbour.

Mary Curran, who also heads the "locally run community" campaign, is behind a petition before state parliament calling for action. It currently has almost 2,000 signatures.

"The main game is to rid the harbour of junk boats, redundant eyesores, decaying wharves and jetties, and to protect marine life from toxic pollutants," she said.

"Simply put, it's a war on wrecks and ruins."

Ms Curran said some of the boats "haven't moved for a decade".

The petition has been backed by residents, organisations including Clean Up Australia, and councils such as the City of Sydney, Inner West Council, North Sydney Council and Woollahra Municipal Council.

Inner West Council Mayor Darcy Byrne said there was "strong support right throughout Sydney for getting this fixed".

"We've had local people telling us for years and years that they just don't understand why abandoned vessels would be allowed to litter Sydney Harbour in this way," he said.

"The maritime agency or authorities have ignored this for far too long. We're calling on Transport for New South Wales to bring this to an end, to get this fixed, and to clean up Sydney Harbour."

The issue was debated in the NSW Legislative Assembly last month with the introduction of the Marine Safety Amendment Bill, which will amend the Marine Safety Act. The bill amends the definition of 'unsafe vessel' and requires any vessel on state waters to be registered.

It means the government will have greater powers to deal with derelict vessels.

Transport for NSW says process to remove vessels 'lengthy'

NSW Maritime, who is responsible for managing the waterways and providing safe navigation for ships in the harbour under the Marine Safety Act, is headed by Transport for NSW.

Transport for NSW said removing vessels can take a long time and there was preference for the owner to act before the state intervened.

"In general, processes are lengthy and allow time for the vessel owner to take appropriate action which, where possible is the desired outcome thus not requiring the state to take action and potentially undertake a debt recovery process," a department spokesperson said.

"Some vessels may be perceived as derelict but which may have current certificates of survey or operation but do not get used frequently and are subject to long term plans for restoration or change of use which may not be noticeable to a casual observer.

"Others may be lawfully moored within a private or leased area and as such, not come under the scrutiny of Maritime staff for some time."

Transport Minister Jo Haylen declined an interview or comment.

Abandoned vessels in the harbour have caused issues in the past.

In August, a houseboat caught on fire in Berrys Bay — a site for derelict vessels.

The boat was stationed next to the decaying Flanagans Afloat — a former floating restaurant in the 1970s — and the SS South Steyne.

Authorities managed to extinguish the flames before they spread to the other ships.

Two years ago, the former Manly ferry, the MV Baragoola, sank next to the Cape Don, an old research vessel and lighthouse tender.

The Baragoola was last in service almost four decades before it sank.

Mr King is worried the MV Cape Don, which has spreading rust and visible holes along the hull, could share the same fate.

"There's holes in the hull of this vessel and I'm very concerned it will go the same way as the Baragoola did, and it will be a taxpayer problem to recover," he said.

The Sea Heritage Foundation, which oversees the Cape Don, said the charity had a long-term plan to dry dock the ship.

"The foundation is in phase two of a three phase program towards dry docking the ship to extend its life and give back to the community," CJ Manjarres-Wahlberg, the organisation's chairman, said.

While the foundation was aware of the holes and rust on the ship's exterior, Dr Manjarres-Wahlberg said there had been repairs "completed on the inside".

"The community and harbour users can be assured that the vessel is structurally sound," he said.

He added that there had been "several underwater marine surveys overseen by certified marine engineers and surveyors" and "three above water surveys by independent third parties".

Environmental impact of aging boats

Besides being a potential safety hazard, abandoned boats also have an impact on the marine environment, according to Bill Ryall, one of the state's leading contamination experts.

Dr Ryall released a paper on the environmental impacts of aging vessels after observing boats in the harbour that were in "bad physical condition".

"There was evidence of rusting on the vessels. What rusting means is that any protective paints that were there have gone into the water and probably into the sediments beneath," he said.

"All of these vessels would have been painted with some kind of antifoulant. The older ones would have tributyltin, which is now banned worldwide."

According to Dr Ryall, tributyltin has "very deleterious effects" on organisms living in the sediments below, with the compound capable of changing the sex of sea snails.

Tributyltin was one of several biocides, which contain heavy metals and organic compounds, found on boats.

"The major concern is the marinas are all shown to contain high concentrations of these antifoulant chemicals," Dr Ryall said.

"Vessels have been here for six years just sitting, and the concentration of chemicals beneath them would be expected to be elevated and causing a real risk of harm to the marine environment."

Dr Ryall said that this matter was something he had "tried to get action on for a number of years", to no avail.

For Mr King, Ms Curran and others involved in the campaign, their push to clean up the harbour continues.

"It's like dumping a car in a national park and expecting everyone to be OK with that," Mr King said.

"I'm not OK with dumping a car in a national park, and we should be treating our beautiful harbour with the same outlook."