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In the Basin of Mexico, one of the most important economic regions in the country with over 22 million inhabitants, peri-urban streams have been transformed into sewers, drains, and pipes to avoid flooding or unsanitary conditions; the change affects not only the ecosystem's goods and services but also the aquatic communities that support the natural ecological processes. We aimed to develop a diatom-based diagnosis of the ecological quality of these aquatic ecosystems through the study of epilithic diatom response to regional environmental gradients. Samples of epilithic diatoms and water were collected in 45 sites representing 12 perennial streams, and multivariate analyses were performed on environmental and biological data. The ecological quality gradient to which diatoms responded was related to oxygen saturation, soluble reactive phosphorous, dissolved inorganic nitrogen, and hydromorphological quality. Three species groups were recognized according to their ecological preferences along CCA1 axis, indicators of high and low ecological quality, and tolerant species. By assigning an indicator value to each species group, we calculated the DEQI using the formula adapted from Pantle and Buck, indicating five different ecological quality classes. This index is proposed for complementing the ecological quality evaluation as a biological metric that responds to multiple regional stressors of the structure and function of these peri-urban streams in the Basin of Mexico. [ABSTRACT FROM AUTHOR]