Macroinvertebrates play a key role in freshwater food webs, acting as major links between organic matter resources, primary consumers (such as bacteria), and secondary consumers (e.g.fish, amphibians, birds, and reptiles). In this paper we present a data set encompassing 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, highlighting the still poorly investigated biodiversity of Italian mountain lake macroinvertebrates. Since they function as key elements to characterize lake ecological status, our data set emphasizes the huge taxonomic effort that still has to be undertaken to fully characterize these ecosystems. The data set is available in csv (comma-separated values) format.