The influence of water quality on the variation patters of benthic macroin-vertebrate communities in the lakes in the central highlands of Peru was eva-luated. Samples of water and sediments were collected in 23 different sam-pling sites last 2017. The physiochemical variables of water quality deter-mined on site were: DO, TDS, EC, temperature and pH. The results obtained revealed that the physiochemical indicators are within the environmental quality standards for water, except COD and BOD₅. Regarding the benthic macroinvertebrates, four phyla were identified wherein the most common is the phylum Arthropoda having the abundance and richness of taxa. The PCA reduced the variables to a few significant components that caused variation in water quality between lakes. The cluster analysis in relation to the relative abundance of benthic macroinvertibrates grouped the 22 sampling sites into three groups with the similar characteristics. The PCoA analysis of the ben-thic macroinvertebrate communities showed a clear separation of sites. The SIMPER analysis at the family-level showed the distribution of the most common species. Therefore, at a significance level of 0.01 it demonstrates that there are significant differences between the number of species and abun-dance of the areas that were evaluated.