The investigation led by the BBC’s Watchdog programme, sent an undercover team to 10 branches each of JD Wetherspoon, Harvester, Slug & Lettuce, Hungry Horse and Marston’s pubs.
Investigators revealed that samples collected found bacteria levels that were "too high to count" at all of the establishments.
Among those bacteria, coliforms, including faecal coliforms – bacteria usually found in the gut and associated with faeces – were present in samples of either ice or soda.
Upon presenting the results to the public, Watchdog presenter Nikki Fox labelled the findings "disgusting" and "worrying".
"These results are really disappointing," she said.
"I don’t think most people would expect this type of bacteria to be present in things we're actually consuming – and certainly not in some of the biggest names in the business.
"What we’ve found suggests that the procedures all these chains have in place aren’t always being followed at a local level."
Cause for concern
Tony Lewis, of the Chartered Institute of Environmental Health, who analysed the findings, suggested bacteria in such high concentrations, and the presence of coliforms, could indicate failings in cleaning standards.
He explained it may even represent a potential risk to health, particularly for people with weakened immune systems.
"Ice is like any other food," he added.
"We consume it, we ingest it, it goes into our stomachs, into our guts, and if it’s loaded up with the wrong type of bacteria then it can make us ill.
"On the basis of the chains that we’ve looked at, the industry needs to do better, making sure that their cleanliness is being well managed."
The findings come almost 18 months after Watchdog found traces of faecal bacteria present in the ice at high street coffee shops including Starbucks, Caffè Nero and Costa Coffee.
All of the pub chains have responded to the shocking investigation findings.
Marston’s said it was "disappointed and surprised at the results", and added an immediate audit, refresher training for staff and internal tests would be done in response.
Hungry Horse also said it had begun an internal investigation and had deep-cleaned all ice and soda equipment.
Slug & Lettuce, a Stonegate-owned pubco, said it was re-investigating the claims made by the programme, had commissioned audits and "reiterated our processes to all sites".
JD Wetherspoon said the company would "take on board the findings of the report".
Harvester said cleanliness and hygiene was of "critical importance" at their restaurants.