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.

The dataset contains more than 3800 occurrence data divided among 9 Eunis species groups (Algae, Amphibian, Birds, Cyanobacteria, Fishes, Flowering Plants, Invertebrates, Protists, Reptiles). Data refer to alien species and native species distributed within 23 sites and 4 Eunis habitats (level 2) all around Italy.

The dataset includes 46,549 records of monogonont rotifers from about 1800 papers published between 1960 and 1992, compiled from De Ridder (1986, 1991, 1993) and De Ridder & Segers (1997).

The dataset contains abundance and body size data of fishes and invertebrates communities of 3 coastal lagoons located in south Italy: Lesina, Varano and Alimini. Data refer to 59 taxa and 32308 individuals.

The dataset contains abundance and body size data of the benthic macroinvertebrates communities of 3 coastal lagoons located in south Italy: Lesina, Varano and Alimini. Data refer to 69 taxa and 52112 individuals.

The dataset contains taxonomic and body size data of benthic macroinvertebrates collected during the spring 2005 in 15 Mediterranean and Black Sea transitional water ecosystems. Data refer to 188 taxa and 34492 individuals.

The dataset contains abundance and body size data of the benthic macroinvertebrates communities of 12 coastal lagoons located in five different countries (Italy, Albania, Greece, Bulgaria and Romania). Data refer to 262 taxa and 53637 individuals.

The dataset contains abundance and body size data of the benthic macroinvertebrates community of the Lesina lagoon. Data refer to 21 taxa (15 species, 2 genus, 2 family, 2 subclass) and 9595 individuals.

The dataset contains abundance and body size data of benthic macroinvertebrate community of the Acquatina lagoon (Apulia, Italy). Data refer to 50 taxa and 14735 individuals.

The dataset contains abundance and body size data of fish community in Acquatina lagoon. Forty-five taxa were recorded, encompassing 9 orders and 20 families, all identified at the species level except two individuals, identified respectively at the genus (Pomatoschistus) and family (Labridae) level. A total amount of 99,995 individuals were collected, and the community was dominated by the species Atherina boyeri, with 95,237 individuals found.