This dataset contains information about water quality based on faecal indicators at eighteen lakes in each of three lake districts: - Greater Glasgow conurbation, Scotland - Cumbria, NW England - Norfolk, E England. Lakes were sampled once in each of three seasons (spring, summer and autumn) in either 2016 (Norfolk) or 2017 (Cumbria and Greater Glasgow) with faecal indicators being quantified at three discrete sampling stations in each lake (>50m apart) and at three points at each station (i.e. nine samples per lake per sampling date). Faecal indicators were quantified based on standard dilution, membrane filtration and incubation, followed by colony counting. The data were collected to investigate the fine scale connectivity between Faecal Indicator Organisms (FIO) densities within water bodies and diffuse and point source inputs from the adjacent catchment and from biological vectors. They also provide an indication of the relative sources of variation in reported concentrations that is relevant for environmental regulatory purposes. The work was supported by the Natural Environment Research Council grant NE/N006437/1 (Hydroscape: connectivity x stressor interactions in freshwater habitats).