Stemming the inputs of microplastic debris into the marine environment is a key societal challenge. Mussels are voracious filter-feeders, which provide an environmentally friendly means of removing waterborne pollutants (e.g. nitrates) and improving water quality. Here we explore whether mussels could be implemented as part of a nature-based solution to microplastics, stemming the flow of plastic particulates and microfibres from source to sea. We employ an interdisciplinary approach, comprising controlled laboratory exposures, modelling and stakeholder engagement, to evaluate the rate at which mussels can remove microplastics under different flow conditions, predict the fate of these microplastics and consider the practicalities of deployment. A custom-designed flume tank was used to demonstrate mussels (Mytilus spp.) can act as biological filters, efficiently removing waterborne microplastics from flowing water and repackaging these plastics into their faeces and pseudofaeces. Further laboratory experiments and computational modelling show microplastics-laden mussel faeces will rapidly sink out of the water column. We propose mussels could be used as an efficient, low-cost and environmentally friendly means of removing waterborne microplastics near source.