This dataset contains information about water quality based on faecal indicators at 15 lakes in the Greater Glasgow conurbation, Scotland. Lakes were sampled in winter (2016/17) and summer (2017) with faecal indicators being quantified at high spatial resolution (up to 60 points per lake depending on water body size) in sediment and water from each lake. Faecal indicators were quantified based on standard dilution, membrane filtration and incubation for water, and incubation in bacteria-specific broth, followed by plating and incubation for sediment extracts. Contextual information about water quality, water bird densities, and land cover in different buffer sizes is also provided for each lake. The data were collected to investigate how connectivity and stressors interact to determine biodiversity and ecosystem function in freshwaters. The work was supported by the Natural Environment Research Council grant NE/N006437/1 (Hydroscape: connectivity x stressor interactions in freshwater habitats)