This dataset contains operational taxonomic units for epilithon eukaryotes (water samples): Approximate location of sampling sites was determined from maps to provide good spatial coverage of the Wolf River through to the Tamar River. Exact sites were determined in the field, considering accessibility and other logistics. The exact location of each sample site was determined using a Garmin GPS12. Three stones were taken from each of the 20 locations and epilithon removed from a defined area. Samples were kept in the cold and removed to the laboratory for analyses. DNA was extracted from all soil and epilithon samples using the MOBIO Powersoil 96 well DNA extraction kit. DNA was quality checked for purity and yield prior to submission for 454 pyrosequencing to assess both bacterial and eukaryotic biodiversity within each sample. Following bioinformatic sequence processing, sequencing were clustered into operational taxonomic units (OTU) and the data tables display the percentage of each OTU within each sample. Full details about this dataset can be found at https://doi.org/10.5285/18023db5-25d8-44f7-b291-61869f937367