The two most common E. coli strains found in the testing only come from ruminants, such as cows.
Experts consulted by Fish and Game said the test results showed all these harmful organisms were present at levels that may impact on human health.
Fish and Game New Zealand chief executive Martin Taylor said the results were disturbing.
"We undertook the testing based on local anglers' concerns and began with samples taken from above and below the biggest farms on the Ashley, Selwyn and Rangitata rivers," Taylor said.
"What we found in the first tests was so alarming, we actually did a second round of testing to confirm the findings, as well as consulting health authorities to get their expert opinions.
"The results suggest these organisms are now common in our water ways - if this is the case, then it certainly is concerning from a public health standpoint."
Taylor said with the holiday season about to begin, the test results are a wakeup call.
"In plain language, the results indicate swimming in these rivers could be like playing Russian roulette with the health of you and your family.
"What we have found indicates the proper authorities urgently need to undertake more testing to establish the extent of the problem, along with action to ensure people are kept safe."
He suspected the contamination could largely be blamed on intensive dairy farming in the region, which was now home to 1.3 million cows.
"These test results show that the sheer number of cows on the Canterbury Plains and in areas like Southland and Taranaki are creating not just environmental problems but also human health issues," he said.
"Regional and district councils also need to be doing a much better job of enforcing the rules and protecting our waterways and the New Zealanders who use them."
In response to the tests, ESR said they stressed the importance of the need for a freshwater microbiological survey of New Zealand rivers.
The last time a national survey was completed was almost 20 years ago and since then there have been significant changes in land use, management practices and marked improvements in testing and analysis.
In 2003, the Ministry for the Environment and the Ministry of Health developed Microbiological Water Quality Guidelines for Freshwater Recreation Areas.
But the previous study did not look for antimicrobial resistant organisms nor pathogenic E.coli, such as STEC.
ESR's health and environment general manager Libby Harrison said the level of E.coli bacteria in water had become a proxy for water quality.
Hundreds of millions of dollars were being spent to meet guideline values – and in some regions, 70 per cent of rivers don't meet these guidelines.
What was needed was an updated national microbiological survey and a revised risk assessment to determine the relationship between microbial indicators and pathogens.
"What this latest report in the media highlights is that a survey is well overdue because of the important relationship of the health of our rivers to public health," Harrison said.
"It will also help ensure that the significant amount of money being spent by councils and the public to meet water quality guidelines is appropriately targeted, based on the latest science."
