Insects of the Chironomidae family are characterized by a wide ecological diversity in freshwater ecosystems. The larvae have the physiological potential to tolerate environmental stress even when there is a low concentration of oxygen, the presence of toxic substances or when there are changes in temperature and salinity. On the other hand, it is important to consider that at a cellular level, when individual insects are exposed to environmental changes, it induces responses of groups of genes that govern the molecular mechanisms related to such tolerance. In this review, using fourth instar larvae of Chironomus spp. in natural conditions and of Chironomus columbiensis under controlled conditions, we will discuss the genetic expression of a group of genes that respond to detoxification and also the biological functions involved and impacted on by mining stressors. The study of macroinvertebrate bioindicator species and their gene expression as a result of mining activity opens a window on the search for genetic biomarkers that could be used in environmental pollution assessments in freshwater ecosystems.