In order to analyse the effects of bio-geo-chemical factors on bacterial freshwater communities on a large scale, 280 lakes were sampled. The sampling of 255 European freshwater lakes was conducted in August 2012, covering a broad latitudinal gradient ranging from Spain to the South of Scandinavia. The samples were taken by daylight from the shore of each lake or pond collecting epilimnial water up to 0.5 m depth. Amplicon sequences target the V2-V3 region of the 16SrRNA gene.