The highest levels of infection were caused by common antidepressants and antifungal medicines.
The team spent two years of testing insects living in the streams, as well as spiders that naturally plunder insects. Almost everyone had significant drug concentrations.
"The most worrying thing was that these insects did not have only one drug – they were up to 69," says Dr Erinn Richmond, head of the Monash University Water Research Center.
"These insects have drugs in really high concentrations, and they carry these compounds into spiders."
It is not certain that human drugs end up in waterways, but the group suspects that they enter the drainage system via human urine and then do not fully filter.
So far, the largest number of drugs found was in Brushy Creek, which receives treated water from a nearby sewage treatment plant.
Dr Richmond said that although the study did not check the drinking water basins, the findings surely raised questions about whether the infection had reached drinking water. Sassafras and Lyrebird Creeks form a small part of the city's drinking water basin.
Using data on the natural diet of platypus, the team estimated that one who lives in Brushy Creek and eats infected insects would take about half a daily dose of antidepressants from humans plus 21 other drugs (the study did not directly check the broadleaf).
"From what we see, it's definitely a chance – but we do not know it and we did not try it."
Melbourne Nea, which partly carried research funding, reports that streams account for less than 0.5% of the catchment area and that all drinking water is rigorously treated and tested for contamination.
The team's findings are stacked up with several other studies, including a study that found pollutants in the water and the Brisbane sediments.
And a major study conducted in 2014 found traces of organic pollutants in nearly all 73 river sites tested throughout Australia, with paracetamol and carbamazepine (anticonvulsive) among the most commonly detected.
"The potential effects of pharmaceuticals are not yet well understood," says Associate Professor Bob Wong, who is studying this very question.
"But previous research has shown that in fairly high concentrations, exposure to some human and veterinary pharmaceuticals can have devastating consequences, including sex change in fish and death in vultures."
Professor of the University of Monash, Wong University, has just published a research that showed that fluoxetine, one of the antidepressants detected in significant concentrations of insects in the Melbourne streams, made male mosquitoes more sexually aggressive.
But the Nature the strong findings of the study – including the finding of contamination in a national park – have suggested an error in data collection, said Stuart Khan, a specialist in drug contamination at the University of New South Wales, who advises the World Health Organization on water quality.
Liam is a scientific journalist at Fairfax Media