Despite its proximity to the urban area of San Miguel de Allende, El Charco del Ingenio keeps an abundant biodiversity, enhanced after years of continuous protection and soil conservation works. The extension of the land, as well as the matching topography and humidity conditions, offer a diverse ecosystem in a healthy process of restoration.

Various studies and inventories of the flora and fauna of the site have been carried out, some already published. Among them stands out the magnificent book by Walter L. Meagher and Wayne Colony Wild and Wonderful: Nature Up Close in the Botanical Garden El Charco del Ingenio, published in 2008. Meagher also produced an exhaustive list of the flora of El Charco, which includes a total of 535 species, belonging to 85 botanical families. In association with this floristic study, 51 lichen species were also identified within the reserve (T. Nash et al.).      

Thanks to the work recently completed, El Charco now has biodiversity lists for five faunal groups: 156 species of resident and migratory birds (S. & W. Colony), 32 species of mammals (R. Aviña), 18 species of reptiles and amphibians (R. Hernández), 110 species of butterflies (S. & W. Colony) and 11 species of dragonflies (S. & W. Colony). These registered biodiversity listings provide El Charco with a database to identify species listed as endemic, endangered, or under special protection under Mexico's federal regulations.

The conservation area comprises three clearly differentiated zones, which correspond to three wildlife habitats: the ravine, the scrubland and the wetland.

These three zones that make up the conservation area can be visited permanently, through the network of trails and paths that extends over the entire surface of Charco del Ingenio and Landeta Park.