Here are the datasets for the paper (Automatic quantification and classification of microplastics in scanning electron micrographs via deep learning) accepted by the Science of the Total Environment. The complete training dataset of semantic segmentation and shape classification is in dataset1.zip. The dataset of instance segmentation is present in multiple forms in dataset2.zip. The experiment setting for each micrograph was recorded together with the original SEM micrographs and all ground-truth labels in the file dataset3.zip. Main results were saved in result.zip.