Effective management of the marine environment at continental and global scales relies on interoperable and reusable data. Stereo imagery is increasingly popular for surveying fish and benthic assemblages due to its cost-effectiveness and ability to accurately measure size distributions. A synthesis of stereo-video datasets around Australia revealed common mistakes made during the collection and annotation of stereo-video imagery. We created an open-source tool which runs quality control checks on metadata and annotations of fish and benthic stereo-imagery. Our tool, available as both a web app and an R package, enables users to compare annotations with taxonomic databases, expected spatial distributions, and maximum body sizes. It offers instant feedback on species found beyond their known geographical range, updated scientific names, and outliers in body size. CheckEM standardises, cleans and visualises stereo-video annotation datasets, offering interactive plots and tables in a graphical interface. It provides downloadable summary data and error reports, facilitating the creation of synthesis datasets from multiple annotations. Rapid, cost-effective and robust environmental reporting at continental and global scales hinges on FAIR data. CheckEM enhances the interoperability and reusability of stereo-video annotations for fish and benthic assemblages, fostering more efficient collaborations among researchers in the future.