This resource contains a checklist of the benthic macroinvertebrate community sampled biannually from 1999 to 2010 in eight natural lakes from the middle Rio Doce Valley lake system and eight river segments in the Piracicaba River basin (sub-basin of Doce river), Minas Gerais State, Brazil. Three of the lakes are located inside a protected state park and are surrounded by preserved vegetation (Atlantic Forest). The other five lakes are in private properties, surrounded by Eucalyptus plantations. The seven stretches of rivers have a distinct degree of anthropogenic impacts. Samples were collected with a kick net and fixed with formaldehyde solution. Four phyla were represented: Mollusca, Annelida, Arthropoda, and Platyhelminthes. For Insecta, 76 families were identified, one family was identified for Crustacea, and nine families were identified for Mollusca. This subproject belongs to the International Long-Term Ecological Research Project (ILTER—Programa de Pesquisas Ecológicas de Longa Duração—PELD) site 4.