The data includes concentrations of faecal indicator organisms isolated from the plastic waste and natural substrates found on Scottish beaches, as well as the antibiotic resistance of selected strains of these organisms. Sewage-associated plastic waste, and naturally occurring substrates (seaweed and sand), were collected in 2021 from ten beaches along the Firth of Forth estuary (Scotland, UK). The concentrations of faecal indicator organisms (FIOs), E. coli and intestinal enterococci (IE), and potential human pathogens (Vibrio spp.) on the plastic waste and natural substrates were analysed using selective media. Minimum inhibitory concentration (MIC) analysis was used to determine antibiotic resistance in selected strains. Full details about this dataset can be found at https://doi.org/10.5285/9d0a6437-f01e-4cf3-9f83-86d2f4ead869