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The dataset encompasses all geographic and historical data available on macroinvertebrates of the Italian mountain lakes from 1902 to 2016. The data set, divided per Italian mountain range (Alps and Apennines) and administrative region, covers more than a century of studies of many foreign and Italian scientists. The data set includes 2372 records and shows macroinvertebrate occurrence data in 176 Alpine and in 13 Apennine lakes, of which 178 of natural origin, 5 reservoirs, and 6 artificially extended. The data set lists 605 taxa, updated on the basis of their current taxonomic position. Only 353 taxa are identified at species level.