The quality of the aquatic environment of high Andean lagoons was evaluated by means of multivariate statistical methods in two contrasting climatic periods. The water samples and benthic macroinvertebrates were collected in 22 sampling sites during the rainy and dry seasons. In each lagoon DO, DTS, EC, temperature and pH were determined in situ. The results revealed that the physicochemical parameters comply with the environmental quality standards for water, except COD and BOD5. In the PCA of the physicochemical parameters, the first two axes explained 73% of the total variation. The gradual analysis in pairs showed significant differences. The SIMPER analysis determined an average of four families of benthic macroinvertebrates per lagoon that showed more than 70% contribution. The ANOSIM revealed that Tragadero lagoon differs significantly from the others. The DistLM showed a value of 0.46 of coefficient of determination. Therefore, the quality of the environment of high Andean lagoons evaluated by means of multivariate statistical methods presents important differences or dissimilarities not only in the physicochemical characteristics of the water, but also in the composition of the benthic macroinvertebrate communities.