A ban on the use of antibiotics in farm animals is being advocated by health and animal welfare groups.
If antibiotics are routinely used in livestock, it can lead tobacteria becoming resistant and such'superbugs' could be passed on to humans.
They carried out tests in the rivers and chicken litter.
New restrictions on antibiotic use are being considered.
The Department for Environment, Food & Rural Affairs doesn't support routine preventative use of antibiotics in animals and will continue to look into strengthening legislation in this area.
UK farming is a leader when it comes to the use of antibiotics.
One of the biggest threats to global health, food security, and development today is antimicrobial resistance.
The rise of'superbugs', strains ofbacteria that can no longer be treated with certain drugs, is a result of the over use of antibiotics.
According to the latest data published by the UK Health Security Agency, the number of serious antibiotic resistant infections in England increased from 52,842 in 2020 to 53,985 in 2011.
The Alliance to Save our Antibiotics and World Animal Protection carried out tests in rivers, pig and poultry farms, and dairy farms to see if there were any superbugs.
They said they found genes that were resistant to antibiotics.
Five of the eight intensive farms had higher levels of resistance found downstream. None of the outdoor pig or chicken farms tested had higher levels of resistance than was found upstream.
The report concluded that factory farms are likely to discharge resistance genes and superbugs into public waterways.
A high number of animals kept closely together can be a breeding ground for disease and can lead to antibiotics being given to whole herds or flocks just to keep illness at bay.
Ciln Nunan is an adviser to the Alliance to Save Our Antibiotics.
Antibiotics taken by people or animals are flushed down the toilet. He said that when manure is spread on land it increases the number of resistantbacteria in the soil and water.
Large cuts to antibiotic use is the best way to reduce farming's impact.
According to Professor Durance, who was not involved in the study, faecal matter entering water bodies can carry with it drug-resistantbacteria and genes.
There is an amount of faecal material in the wastewater. There is a way to have chickens that are healthy and resistant to antibiotics. She said that once there is faecal material in the water bodies there will be anti-bacteria.
She said it was difficult to link thebacteria in rivers to a specific source.
Antibiotics are only used on higher-welfare outdoor farms when sick animals are in need and not as a preventative measure, according to the co- founder of the farm.
He said he was not surprised by the report's conclusion. The excreta that comes out of an industrial pig or poultry environment is spread so that it can feed into the river. The balance of nature is disrupted due to that.
The EU banned all routine farm antibiotic use and all preventative antibiotic treatments of groups of animals in order to tackle the over use of the medicines.
The government supports a ban, but hasn't carried out the public consultation it promised.
Changes to the regulations on antibiotic use on farms will be put out for public consultation.
Sales of antibiotics for use in livestock have reduced by more than 50% in the last two years, according to the latest annual UK veterinary antibiotic resistance and sales data.
The Responsible Use of Medicines in Agriculture (RUMA) Alliance's Cat McLaughlin said that livestock farmers were making positive progress on antibiotic use reduction targets.
She said that antibiotics are important tools that the veterinary sector needs at its disposal.
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