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Sales of single-use plastic bottles will be halted on the Museum's sites in South Kensington and Tring.
Over the following months, staff will assess how to provide visitors with improved access to water fountains and encourage people to refill their bottles and cups instead of buying disposables. Reusable bottles will also be on sale.
The move comes amid growing concern from many scientists and environmentalists, including those working for the Museum, about the impact of plastic on the world's oceans.
Research by Museum scientists, conducted in collaboration with Royal Holloway in 2014, has shown the extent of unseen plastic pollution in the Thames and the presence of plastics in the stomachs of fish.
Billions of tonnes of plastic are dumped into the ocean each year. Earlier in 2017 it was widely reported that one million plastic bottles are bought every minute. Rather than being recycled, the majority of those end up in landfill or the ocean.
Professor Ian Owens, Director of Science at the Museum, made the announcement at the Annual Science Lecture, the Museum's flagship science debate that this year focused on marine conservation.
He says, 'It's vital that scientific institutions like the Museum lead the way in the fight to understand and protect the natural world.
'The scale of ongoing plastic pollution is having a devastating effect on many marine species and the ecosystems that sustain life on Earth. Millions of single-use plastic bottles are purchased every day in the UK alone, and billions end up in the sea every year.
'Our decision to stop selling single-use plastic water bottles is about becoming part of the movement towards a refillable culture. We are doing our part to encourage a mass lifestyle change that will help reduce the deluge of plastic into our seas.'
Cafes at both Museum locations stopped offering plastic straws to visitors in 2017, and staff are looking into further ways to reduce the on-site use of plastic. Staff and visitors can already recycle plastic bottle waste responsibly at the Museum.
Sarah Dobson, Environmental and Sustainability Officer, says, ‘The Museum works hard to continually reduce the impacts our operations have on the environment.
'Moving away from single-use plastic is an important, visible first step in publicly considering the impacts of our resource use and leading staff and visitors on our journey to a more sustainable future.'