Conservation and management of aquatic ecosystems that are significantly influenced by urban activities requires the classification and establishment of potential reference sites. However, in Latin American countries, policies are not available that outlines the identification and evaluation of such sites. Therefore, this study represents a proposal for evaluating the ecological quality of peri-urban rivers in the conservation soil (CS) areas/zones of Mexico City. The proposal accounts for the zone’s physicochemical, hydromorphological, and bacteriological characteristics along with its macroinvertebrate richness. Our evaluation was performed using a canonical correspondence analysis (CCA) and indicator values (IndVal) calculated for different species. River headwaters serve/work as a good physicochemical point for potential references sites. However, the hydromorphology of the CS has been gradually modified by numerous hydraulic alterations within the peri-urban zone. Using the CCA and IndVal, two types of sites were confirmed: sites in a good state of conservation and quality and sites modified by human activity, featuring lower discharge flow, poor quality hydromorphological values and Oligochaeta class organisms. At the sites featuring a good state of conservation and quality, higher hydromorphological values were positively correlated with discharge flow and certain macroinvertebrate taxa, including Nemouridae, Podonominae, Tanypodinae, Acarina, Baetis, Tipula, Antocha, Atopsyche, Glossosoma, Polycentropus, Hesperophylax and Limnephilus. In the sites modified by human activity, the genus Simulium was classified as a disturbance-tolerant organism. The river reach within the urban zone is basically an open-air drainage ditch. Evaluations of the ecological quality of the riparian zone were used to identify the most important hydromorphological qualities and discharge flow parameters and to select the most appropriate factors that should be monitored in peri-urban rivers of the Mexico Basin.