Pollution teams on Thursday were still clearing up the Thames in west London four days after 450,000 tonnes of raw household and industrial sewage overflowed into the river. The incident, which occurred after nearly 30mm of rain fell in a few hours on Sunday, killed tens of thousands of fish and left condoms, faeces and other pollution on riverbanks.

There are fears that a similar incident could mar the Queen's Jubilee celebrations next June when 1,000 ships from around the world will travel with the Queen as she makes her way down the river in a new royal barge to celebrate 60 years on the throne. The chances of the Royal procession having to make its way through a tide of pollution is considered "very unlikely but conceivable", according to sources in the Environment Agency.

There are on average more than 60 significant sewerage incidents a year in the river, with major ones becoming more frequent. Heavy rains after dry spells left the river massively polluted in both 2004 and 2009. In the latest incident, 250,000 tonnes of storm sewage overflowed into the river from drains and a further 200,000 tonnes from the Mogden sewage treatment works in Isleworth. In response, the agency has spent four days pumping oxygen and hydrogen peroxide into the water to try to build back its health.

"This was a very big incident. Much of south-east England could be affected because the tidal Thames is a vital fish nursery for the whole region. There were a lot of juvenile flounders killed, who use the river as a nursery ground. Roach, dace, bream, eels, perch, pike, sea bass and flounder were all killed," said Angling trust's chief executive, Mark Lloyd.

Steve Holmes, a member of Thames Anglers' Conservancy, said he tried to help dying fish by Barnes Bridge. "We saw literally thousands upon thousands of small fish gasping for air on the surface. Many bigger fish had beached themselves."

The incident comes less than a year after the Thames won a global conservation prize for its dramatic recovery after being declared biologically dead in the 1950s. The International Thiess river prize, awarded annually in Australia, saw the Environment Agency receive a prize of £218,000.

Sewage floods into the river as many as 60 times a year because the antiquated, Victorian-age drainage system is unable to handle the quantity of sewage that London now produces.

Thames Water is planning to build the Thames Tideway "super sewer" to collect sewage before it overflows and channel it to a treatment plant, but the £3.6bn 20-mile tunnel along the river bed is not expected to be operational until 2020.

Martin Baggs, chief executive of Thames Water, said in a statement that the company "very much" regretted the fish deaths and environmental damage caused by the sewage. "Incidents like this are clearly totally unsatisfactory in a modern capital city and we have a major programme of work under way to sort the problem out", he said.

Britain agreed to meet EU water quality targets in 1991 but has so far failed to do so.