Data gathered by environmental campaign group Surfers Against Sewage (SAS) showed that the south-western and southern coasts of England were the worst affected.
Due to sewage overflows, swimmers are advised against bathing at seven beaches in Cornwall, with four in Devon and five in Dorset also polluted during the recent downpours.
Nine beaches in Sussex, three on the Isle of Wight and three in Essex were also hit by storm sewage.
Elsewhere, there were warnings in place at spots in Lincolnshire, Cumbria, Lancashire and South Wales, as well as two inland wild swimming spots near Bristol and near Minehead in Somerset.
On Tuesday, there was an alert at Spittal near Berwick in Northumberland, although this has since cleared.
There has been growing public outrage in recent years over the volume of raw or partially treated sewage pumped into the UK’s rivers and coastal waters.
Hugo Tagholm, chief executive of SAS, tweeted on Tuesday: “The [storm] after the calm. Many south coast beaches off limits due to @SouthernWater sewage discharges.”
A spokeswoman for SAS said there were a further nine pollution warnings in places not linked to heavy rain, and those visiting the coast are advised to always check the interactive map on the organisation's website before they swim.
In a report published in July, the Environment Agency said water company bosses should face prison for the worst pollution incidents, describing the sector’s performance in 2021 as the “worst we have seen for years”.
“The current risk of surface water flooding reinforces the need for robust action from water companies to reduce discharges from storm overflows,” said an Environment Agency spokesman said on Wednesday.
He added that the agency is monitoring the current situation and supporting local authorities where needed.
“Yesterday’s thunderstorms brought heavy rain which fell on to parched ground and couldn’t absorb surface run-off, meaning that more rain than usual overwhelmed our network,” said a spokesman for Southern Water.
“This led to some overflows — which are used to protect homes, schools, businesses and hospitals from flooding — spilling excess water into the sea in parts of West Sussex, including Seaford.
The spokesman added that the discharge is heavily diluted and typically 95 per cent of it is rainwater.
“We are dedicated to significantly reducing storm overflows and are running innovative pilot schemes across the region to reduce the amount of rainfall entering our combined sewers by 2030.”
The spokesman said a viral video showing raw sewage apparently being pumped into the water at Seaford, East Sussex, was in fact surface water run-off.
“During the heavy rain earlier this week, a short discharge of stormwater was made from a storm overflow at Spittal, near Berwick. Such discharges are mostly rainwater with a small percentage of wastewater that have come together because they use the same sewer network,” said Northumbrian Water.
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“At times of heavy rainfall, all water companies use storm overflows as a relief valve on our sewer network to protect the homes of customers and the environment from sewer flooding. Such discharges happen with both permission and scrutiny from the Environment Agency.
“In the last Bathing Water classifications released by Defra, 32 of the North East’s 34 designated bathing waters achieved either ‘excellent’ or ‘good’ ratings, with Spittal in the highest category.
Northumbrian Water added that is has invested heavily in upgrades to its wastewater network in the past two decades, which played an important part in these results
“More than £80 million of investment is targeted towards improvements related to storm overflows in our current 2020-25 operating period,” it said.
Anglian Water, which supplies Lincolnshire and also provides wastewater services at Southend, said: “Combined storm overflows (CSOs) were originally designed to protect homes and businesses from flooding during heavy rainfall, like we saw last night.
“In parts of our region last night, we saw almost 100 millilitres of rainfall in only a few hours. That’s the equivalent of well over a month’s worth on to ground that is essentially like concrete.
“As it’s been dry for so long, intense rainfall on to hard ground will not soak in and instead runs straight off.”
A spokeswoman said any discharges would predominantly have been rainwater and added that its BeachAware system had notified SAS of the discharge “as a precaution so people can make educated decisions about swimming in the sea”.
“However, we recognise that they are no longer the right solution when sewers become overloaded with rainwater,” she added.
“We’ve been dealing with CSOs for years, tackling those which pose an environmental risk and working through the rest.
“Between 2020 and 2025, we’re investing more than £200m to reduce storm spills across the East of England and, as part of our Get River Positive commitment, we’ve promised that storm overflows will not be the reason for unhealthy rivers in our region by 2030.”
Other water companies in areas where there are sewage alerts have been approached for comment.