Pesticides that harm bees were found in the “majority” of English waterways tested in the last year, according to data analysis by two environmental charities.

The Rivers Trust and Wildlife and Countryside Link found neonicotinoid pesticides were present in 85% of English rivers tested by the Environment Agency between 2023 and 2024.

The banned pesticide was signed off for emergency use by the previous government to combat a disease impacting sugar beet crops – a decision for which the Department for Environment, Food and Rural Affairs’ (Defra) is now being investigated.

On Monday, the government promised “to ban the use of neonicotinoid pesticides that threaten bees and other vital pollinators.”

The Office for Environmental Protection is currently investigating Defra’s emergency authorisation for the use of a type of neonicotinoid on sugar beet seeds in 2023 and 2024.

The watchdog is exploring whether the government failed to comply with environmental laws when it previously granted the use of the banned pesticide.

Neonicotinoids are a group of insecticides used in agriculture, horticulture and veterinary medicine to control pests – but they also harm bees and other beneficial insects.

They are currently used by sugar beet farmers to protect their crops from virus yellows, a disease spread by aphids.

In March, Dan Green, agriculture director for British Sugar, said the pesticide was needed “to protect the UK sugar beet crop and farmer livelihoods”.

But environmental charities are calling on the government “enforce and extend” the ban on the use of Neonicotinoid to protect plant and animal health. The charities are also calling for better river monitoring by the agency.

Dr Richard Gill, principle researcher at Imperial College, said that while high concentrations of neonicotinoids can kill bees, smaller quantities can also have “cumulative, sub-lethal” effects on the pollinators, changing their behaviour and even impacting their genes.

Under the influence of neonicotinoids, bees can struggle to fly, and “seem to bring back less pollen” to their hives, Dr Gill said.

The latest analysis of Environment Agency figures comes against a backdrop of declining bee populations across the country.

A number of factors – including changes in the use of agricultural land, urbanisation, the impact of climate change, pesticide use and emerging pathogens – means many bee species are “not doing very well”, Dr Gill said.

“It is concerning that we’re finding these pesticides in the rivers,” Dr Gill said, adding it was important to monitor the concentration of the chemicals in the waterways.

Amy Fairman of the River Action campaign group said agricultural waste is responsible for a greater percentage of water pollution than sewage in the UK.

She said that while their impact on bees is widely recognised, neonicotinoids also harm marine ecosystems, including river insects.

“River insects are right at the bottom of the food chain,” she told BBC News. “If we’re destroying the bottom of the food chain in our rivers, this is going to have a knock-on effect.”

The chemicals are also “notably quite dangerous to human health”, Ms Fairman said.

She suggested people considering swimming in polluted rivers should “understand the levels of contamination” and “educate” themselves about the risks before entering the water.

The latest analysis suggests a slight increase in neonicotinoids levels compared to previous years.

The Rivers Trust and Wildlife and Countryside Link has pointed out its analysis is based on a small sample size of data provided by the Environment Agency.

The charities are calling for more comprehensive river monitoring by the regulator after only a small proportion of the country’s river sites were tested for neonicotinoids in the last year.

At the Labour Party conference in September, Environment Secretary Steve Reed committed to “restore nature and stop animal waste, fertiliser and pesticide pollution running into our waterways.”

On Monday, a Defra spokesperson said the department is “committed to tackling all sources of pollution to clean up our rivers, lakes and seas.

“This government has been clear that we will change existing policies to ban the use of neonicotinoid pesticides that threaten bees and other vital pollinators.”

The Environment Agency said its testing was “specifically targeted at sites where we want to better understand the chemical risk and any action needed to protect the environment.”