Harmful levels of long-banned chemicals, including the pesticide DDT, have been found in the tissues of two vulnerable dolphin species swimming in waters flowing into the Great Barrier Reef.

Scientists found levels of the chemicals in the tissues of snubfin dolphins and humpback dolphins had tripled and, in some cases, risen even higher between 2010 and 2015.

One tissue sample taken from a female humpback dolphin had concentrations of polychlorinated biphenyls (PCBs) – banned in Australia since 1975 – that were among the highest recorded in the scientific literature.

Scientists at Flinders University and Southern Cross University examined levels of PCBs, DDT and hexachlorobenzene (HCB) in the tissues of dolphins in 2009 and 2010, and then took samples again between 2014 and 2016. They published the results in the journal Ecological Indicators.

Special darts were used to take 5mm-wide samples of blubber and skin from the dolphins while they were swimming at locations in the Fitzroy River estuary and at Port Curtis.

The marine ecologist Dr Daniele Cagnazzi, of Southern Cross University, said 68% of the dolphins sampled had levels of the chemicals high enough to impact their health “and long-term survival”.

He said: “With PCBs, DDT and HCBs – these have been linked to mass mortality events. We know they have health implications and can affect the dolphins’ immune system and make them more susceptible to other diseases.

“These elements have been banned from Australia and many other countries, but because they are persistent contaminants they survive for a long period of time.”

The snubfin dolphin is the only dolphin species unique to Australia, and is listed in Queensland as vulnerable. There were 18 samples from snubfin dolphins analysed for the three pollutants, all taken at the Fitzroy River estuary.

Humpback dolphins are also listed as vulnerable in Queensland. There were six samples analysed from the Fitzroy River and 11 from Port Curtis.

A 2015 sample from one female humpback dolphin from the Fitzroy River estuary had concentrations of PCBs among the highest ever recorded in the scientific literature.

While the study was not designed to find a cause, researchers wrote that flooding in the regions and nearby port developments were likely to be behind the rising levels of contaminants.

Associate Prof Guido Parra, a co-author of the study at Flinders University, said the build-up of contaminants “could have implications on the long-term survival of entire dolphin populations in Queensland”.

He said the threat from the chemicals added to existing problems faced by dolphins, including climate change, habitat destruction, underwater noise and fishing bycatch.

Tooni Mahto, the threatened species campaign manager at the Australian Marine Conservation Society, said: “These dolphins are a unique and vulnerable species and they exist in very small populations. They need protecting.

“These animals are still paying the price of these chemicals that we stopped using almost half a century ago. They are silent killers in the water.”

Dr Liesbeth Weijs, of the Australian Rivers Institute at Griffith University, who was not involved in the study, said the results were indicative of findings around the world. Her own work had found the same rising levels of contaminants in dolphins in South Australia.

She said the contaminants accumulate in the fatty tissues of dolphins through the food they eat – mainly fish.

“These substances were engineered to be persistent – they don’t break down and they were designed to hold on for decades.”