This dataset contains faecal bacteria data (mainly E. coli but also some Intestinal enterococci) for the River Wharfe and its tributaries in Yorkshire. They were collected and analysed as part of citizen science projects (termed the Ashlands and iWharfe projects) designed to assess the extent to which the river is contaminated by sewage effluent and capable of meeting national bathing water standards. In the Ashlands project, samples were taken upstream and downstream of the Sewage Treatment Works in Ilkley. The data were used in a successful application by the Ilkley Clean River Group for the river in Ilkley to be designated as a bathing water, the first running water site so designated in the UK. The iWharfe data are from samples collected on two occasions (2020 and 2021) at sites along the full length of the river and selected tributaries and show in particular the level of faecal bacteria contamination at recreational sites along the river. Overall, the data show not only the importance of sewage effluent in causing high concentrations of faecal bacteria in the river but also the role of agricultural sources presumed to be from farm livestock.