Minimising human faecal organisms in fresh water is a “public health priority as well as an environmental one”, Sir Chris Whitty has warned.

England’s chief medical officer has backed a new report released by the National Engineering Policy Centre, which outlines engineering solutions to the UK’s crumbling water system with a focus on protecting people’s health.

The team of researchers, who worked with wastewater experts, campaigners and policymakers, said the UK’s wastewater infrastructure must be improved to reduce exposure to human faecal pathogens in effluent – treated water released back into rivers, seas and lakes.

People are increasingly using coastal and inland open waters recreationally, leading to greater public exposure to pollutants, the report said.

Ahead of its release on Tuesday, Sir Chris told reporters that “the human health aspect is one of the things that needs to be taken seriously when we’re measuring the quality of water”.

“Minimising human faecal matter is a public health priority as well as an environmental one,” he added.

It comes as a fresh row over water quality broke out last week after confirmed cases of the waterborne disease cryptosporidium in Devon and reports that millions of litres of raw sewage were pumped into Windermere.

Professor David Butler, chairman of the National Engineering Policy Centre working group on wastewater, told reporters: “What we’re saying we would like to see now and in the future is that public health almost becomes one of the pillars… considered alongside affordability – yes – and alongside environment – yes – when making these big investment decisions.”

Sir Chris warned sewage spills during wet periods are “half the problem, not the full problem” because some human faecal organisms also remain in treated water when it is released back into the environment.

“The lower the water, the less they’re diluted out,” he added.

“So if you’ve got a very low river because it’s been dry recently, that’s the ideal situation for children to paddle and people to swim.

“But that is the time… when a lot higher proportion of the faecal organisms will have come out of a sewage treatment works rather than out of storm overflows.”

The report outlined 15 short-term and longer-term recommendations to reduce the amount of human faecal matter going into the environment as well as people’s exposure to any that does.

Professor Barbara Evans, from the University of Leeds, said: “It would be a really good moment to get everybody around a metaphorical table to decide what we’re willing to invest in and why we want to invest in it”.

Recommended short-term actions include improving the maintenance of existing water infrastructure, developing and deploying more microbial and water quality monitoring, and reviewing bathing water standards based on best evidence.

The engineers also suggested a ban on solid materials that clog up water systems, like wet wipes, could free up money used for dealing with blockages on other solutions.

Ms Evans said: “As an engineer, it would mean that we would be much more confident that the system would run well. We can solve this problem more easily if wet wipes are not in the sewers.”

The engineers also suggested introducing incentives to members of the public to remove impervious surfaces in urban areas – like patios or paved-over gardens.

Mr Butler said this would reduce the amount of run-off into the wastewater system but is “also a great opportunity to regreen our urban areas”.

“We think that is one of our win win win solutions which we love in engineering,” he said.

The researchers admitted that there is a lack of evidence to demonstrate a direct, causal link between specific wastewater discharges and specific health incidents but emphasised the known health risks from exposure to high concentrations of faecal organisms.

“We need more research to improve our understanding of what’s going on in terms of this faecal pollution,” Ms Evans said.

Responding to the report, Charles Watson, chairman of River Action said: “We particularly welcome the call for Government to accelerate the roll out of continuous water quality monitoring for microbiological faecal organisms and to conduct a fundamental review of bathing water regulations.

“At present, other than at the miniscule number of designated river bathing water sites, nothing is being done to provide river users with even the most basic information on the dangers they are facing.

“It is imperative that our elected politicians treat this report as a major wake up call given the past failures to protect the public from the rising tide of sewage pollution.”

An Environment Department spokesperson said: “Alongside the Environment Agency securing over £150 million fines to date and quadrupling inspections, we are already driving the largest infrastructure programme in water company history of £60 billion over 25 years, which will drastically reduce spills.

“Later this year we will launch a consultation on reforming our bathing water regulations which will include work to improve bathing water quality and enhance monitoring.”

A Water UK spokesperson said: “Water companies have a plan with proposals to double the current level of spending between now and 2030.

“Public health is a major part of the next phase of the programme, with bathing areas heavily prioritised for investment.”