Plastic pollution is ubiquitous throughout the environment, and its potentially hazardous effects have become of great concern in past years. More than 80% of the plastics enter the marine environment from land-based sources via rivers. To prevent plastic litter from reaching the marine environment, where it spreads rapidly and it is difficult to extract a posteriori, more than thirty plastic clean-up technologies are commercially available to date to remove plastic from inland waters. The focus of these technologies is to collect plastic most efficiently, but less attention is given to their potential bycatch, such as living organisms and organic debris. The organisms and organic debris accidentally and unintentionally bycaught often could provide essential functions in the rivers and estuaries’ ecosystems where clean-up technologies are deployed. River estuaries are regarded as regions of high biodiversity, providing feeding grounds, shelter, and nurseries for some threatened and commercially important species. To date, an objective tool to quantify and assess the bycatch of plastic clean-up technologies is lacking. This study aims to resolve this knowledge gap by creating, with the aid of a probabilistic model, a decision framework for the plastic clean-up technologies. Such a decision framework will guide policymakers and river managers to wisely select the best-suited technology to remove plastics from rivers, while mitigating potential collateral damage.