An unseen stream of plastic rubbish flowing along the bed of the river Thames and out into the North Sea will have far-reaching effects on marine life, a new report indicates.

Scientists from the Natural History Museum and Royal Holloway, University of London, collected rubbish over a three-month period at the end of 2012 from seven locations along the river bed of the upper Thames estuary, between Crossness and Broadness Point.

The team netted 8,490 items including plastic cigarette packaging, food wrapping and cups that may have been blown or washed into the river down storm drains. More than 20% of waste was made up of sanitary products such as pads and plastic backing strips, which had most likely been flushed straight down the toilet. The full extent of the unseen waste could be far worse, the study warned, as plastic bags and other large items may have escaped the small nets used in the study.

The two most contaminated sites were in the vicinity of sewage treatment works at Crossness and Littlebrook, the report found, and could indicate that plants were not filtering out larger waste, or were letting sewage overflow when heavy rains created extra waste.

The report said the data represented only a snapshot, and as such it was difficult to estimate the volume of litter that was actually entering the North Sea this way. But scientists said the figures highlighted an underestimated problem.

"This underwater litter must be taken into account when estimating the amount of pollution entering our rivers and seas, not just those items that we can see at the surface and washed up onshore," said Dr Dave Morritt, senior lecturer in marine biology at Royal Holloway, University of London and co-author of Plastic in the Thames: A River Runs Through It, published in the Marine Pollution Bulletin. "The potential impacts this could have for wildlife are far-reaching: not only are the species that live in and around rivers affected, but also those in seas that rivers feed into."

The team was originally conducting a trial of different types of "fyke nets" – a type of trap anchored to the river bed – that would allow invasive Chinese mitten crabs to be harvested while allowing endangered eels to escape. But they spent so long clearing plastic rubbish from the nets that they thought this alone merited further study.

Plastic rubbish collected in a fyke net, used to harvest invasive Chinese mitten crabs. Photograph: Trustees of the Natural History Museum

The report also warned that larger pieces of plastic are being continuously rolled backwards and forwards by the estuary's tidal movements and broken down into smaller and smaller "microplastic" fragments that are easily ingested by birds, fish and smaller species such as crabs.

This follows a study in December that highlighted the potential impact on ocean ecosystems when species at the base of the food chain ingest microplastics. Lugworms, starfish, sea cucumbers and fiddler crabs all act as prey for birds and fish, transporting the tiny fragments up the food chain. A second study found evidence that potentially harmful chemicals including hydrocarbons, antimicrobials and flame retardants were leaching from the ingested plastic into the digestive systems of such species.

Dr Paul Clark, a researcher at the Natural History Museum and co-author of the study, said: "Plastic can have a damaging impact on underwater life. Large pieces can trap animals but smaller pieces can be inadvertently eaten. The toxic chemicals they contain, in high doses, could harm the health of wildlife."

The findings are the latest evidence that plastic pollution is having as big an impact on freshwater environments as the seas.

The issue of plastic pollution in the ocean environment – where as much as 80% of litter is plastic – has become more high-profile in recent years, with widely documented instances of fish and bird entanglement, ingestion and suffocation and the growing Great Pacific and North Atlantic garbage patches.

But there has been less attention focused on the issue of plastics flowing down major rivers, with only a handful of prominent studies to date looking at the impact on catchments and watersheds.

In October this year a study published in the journal Current Biology found that lake Garda, one of the famous Italian lakes, contained as many microplastic particles as in marine beach sediments. And in 2012 it was found that plastic pollutants circulate in pockets of America's Great Lakes at concentrations higher than any other body of water on Earth.