The world's first research measuring outboard engine emissions in fresh and salt water has found underwater pollutants could be cut by up to 1000 per cent by switching from two to four-stroke engines.

Dr Richard Brown of Queensland University of Technology's School of Engineering Systems found that two-stroke engines produced up to 10 times more water pollution than four-stroke.

He said the cocktail of chemicals outboard motors left in their wake acidified waterways and deposited long-lasting carcinogens.

"Heavy metals can be bound in sediments but as outboards motor emissions lower the pH of the water, heavy metals can be released as the water becomes acidified.

"The heavy metals in the acid water then become bio available and enter the food chain."

Dr Brown measured and compared levels of more than 20 chemicals left in salt and freshwater by two-stroke and four-stroke engines.

He said previous studies had focused on air pollutants produced by these engines but no-one had, so far, looked at what they left behind underwater.

"About 1,000,000 tonnes of oil are released into the world's waterways by ships and boats each year and very little had been known about what was in those emissions and where they went," Dr Brown said.

"We now know we can reduce emissions by 1000 per cent by using four-stroke engines.

"About 80 per cent of outboards are two-stroke, perhaps because they are cheaper to produce, but people are changing their minds about them and in 10 years we hope high emissions outboards will have been phased out.

"In Europe and the United States this is already happening as regulations are becoming much more stringent because of pollution effects in waterways."

The next stage of the research is to do an environmental burden assessment to find out emissions' effects on coastal and estuarine environments with the ultimate goal of achieving an ecologically sustainable water transport industry in Australia, Dr Brown said.