The bottom of Sydney Harbour has been contaminated by widespread microplastic pollution which could be entering the food chain, scientists say.

Professor Emma Johnston from the Sydney Institute of Marine Science said the microplastics, or fragments of plastic less than five millimetres long, represented the "emergence of new contaminants in our harbours and waterways".

In the first study of its kind, 27 sites were tested across the harbour, with researchers discovering up to 60 microplastics per 100 milligrams of sediment.

The environmental effects of the contaminants are largely unknown, but there have been moves to ban their use in products overseas.

Professor Johnston said some of the microplastic contamination was coming directly into the harbour.

Vivian Sim, a PhD candidate working on microplastics at UNSW. ( ABC News, Nicole Chettle )

"For example when we wash our fleecy jackets in the washing machine, lots of particles of microplastics, thin threads, come off and enter our waterways," she said.

"But there are also microplastics from facial scrubs and there are breakdown products from macro debris, like plastic bags or plastic bottles."

A PhD candidate at the University of New South Wales, Vivian Sim, said several hotspots were identified and the worst-affected area was in the pristine-looking waters of Middle Harbour.

"Something interesting is going on here, but we're not sure what," she said.

This map shows the number of microplastics per 100 millilitres of wet sediment found at 27 sites across Sydney Harbour. ( ABC News )

Risk of contaminating food chain

In Middle Harbour, microplastic threads were more common than flakes or balls, but it was unclear where they came from.

"We should be worried about it," Ms Sim said.

"We actually managed to pull up a sipunculid worm today.

"It's got sand going through all of it, so you can see that it's ingesting it.

"So if your microplastic fragments are as small as a sand grain, then [the worm] is going to take up the plastics and contaminants, and then if something else comes along and eats that worm it's going to go further up the food chain."

It was not clear what impact microplastics were having on the organisms that were eating them, but Professor Johnston said some contained materials such as flame retardants.

Sorry, this video has expired Microplastic contamination found in Sydney Harbour ( Nicole Chettle )

"We actually don't know anything about their concentration or what their ecological effects are," she said.

Ms Sim was looking to complete her research this year, but the Sydney Institute of Marine Science said the broader investigation would probably take four years.

Around the world, cosmetic manufacturers are responding to concerns about microplastics and several are phasing out the use of artificial cleansing beads.

Unilever said it would stop using them worldwide by January 2015.

In the United States, Illinois has banned the production and sale of plastic microbeads in personal care products.

"Moves like that will actually end up with far greater effects in our marine systems than we recognise," Professor Johnston said.

"We need to make those changes now to reduce the input of microplastics into waterways like Sydney Harbour."

She said more research was needed to determine the impact of microplastics on the harbour.