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We present a data set on the biodiversity of Italian freshwaters, including lakeshores and riverbanks. This is the first data set on freshwater biodiversity created at national level, including both natural (379 springs, streams and lakes) and artificial (11 fountains) sites. This data set belongs partly to the Italian Long Term Ecological Research network (LTER-Italy) and partly to LifeWatch, the European e-Science infrastructure for biodiversity and ecosystem research. The data included in the data set cover a time period corresponding to the last sixty years (1951-2013). They span a large number of taxa from prokaryotes and unicellular eukaryotes to vertebrates and plants, including taxa that are linked to the aquatic habitat in at least part of their life cycles (like immature stages of insects, amphibians, birds and vascular plants). The data set consists of 6715 occurrence data and distribution records for 1884 species. The complete data set is available in csv file format via the LifeWatch Service Centre.