Pollution washed into Sydney’s beaches and waterways could linger for days, with state authorities urging swimmers to exercise caution after the flood disaster. Sydney Harbour turned brown as a result of storm water carrying soil and debris, and algal blooms have appeared on the usually pristine sands of Hyams beach in the Jervis Bay region. Rainfall is the major driver of pollution into coastal areas because it generates storm water and triggers the overflow of raw sewage into waterways. Flood waters, sediment and debris are behind the murky colour of many waterways along the New South Wales coastline and the viruses and bacteria carried by untreated sewage can pose a health risk to swimmers. “It’s not just the local stormwater that’s polluting our beaches, but it’s the murky water from the flood-affected inland areas,” said Meredith Campey, the manager of the NSW government’s Beachwatch program, which provides pollution forecasts. “It’s flowing downstream into the ocean.” Campey said the greatest effects were on estuaries where storm water was discharging into the ocean and where there were lower levels of flushing. “Places like Pittwater, Sydney Harbour, Botany Bay,” she said. “So it takes longer to recover from the storm water events.” Swimmers are typically advised to avoid swimming in ocean beaches for one day after rainfall, and for three days in harbours and enclosed bays. But given the scale of the flood disaster, Campey said the dangers could linger for longer, noting that flood waters were still making their way through river systems. Swimming in waterways affected by storm water can expose swimmers to pathogens that can lead to illnesses such as gastroenteritis, and ear and skin infections. Beachwatch routinely collects water samples from Sydney’s beaches and estuarine swimming sites, including Sydney Harbour, and tests for bacteria as an indicator of faecal contamination. Recent results have contained elevated microbial levels, showing the effects of storm water pollution and indicating the water is not suitable for swimming in. There is also a risk of injury from hidden objects and debris submerged in the water, such as furniture or trees. “So before you go for a swim, we’d always say to check for signs of pollution such as the flowing drains, discoloured waters, odours and floating debris,” Campey said. Daily beach pollution forecasts are also available on the Beachwatch website. The director of the graduate school of engineering at the University of New South Wales, Stuart Khan, said the colour of the water in places such as Sydney Harbour was largely due to soil and debris in the water. “One of the reasons it looks particularly bad now is because the degree of flooding would have caused a lot of erosion in gardens and parks,” Khan said. He said given flood waters were still making their way down rivers such as the Hawkesbury, there would be some places that would take a while to clear up. “I would be wary until it’s visually clear,” he said. “The recommendation is usually three days but if it’s still brown after a week I wouldn’t be swimming in it.” Sign up to receive an email with the top stories from Guardian Australia every morning The NSW environment department’s director of water, wetlands and coast, Peter Scanes, said fine particles could stay suspended in waterways for a week or longer. Scanes said this would reduce the available light, creating stress for seagrasses, seaweeds and kelps, which provide important habitat. The arrival of fresh water into salt water systems would also create problems for some marine species. “Our marine fish and our estuarine fish, they don’t like to be in freshwater,” he said. “At the moment, the fresh water in the Hawkesbury and probably in Sydney Harbour has pushed out all the salt water at least on the surface.” He said some species will have sought refuge at the bottom of waterways, where the water will still be salty. Others will have been forced to move elsewhere. Scanes said freshwater fish would also be seeking refuge because soils and sediment could irritate their gills, and in places away from the main flow of flood waters “So that they don’t get swept away … they can keep their energy by hiding behind rocks and logs and in backwaters,” he said.