The vast property acquired and the breadth of the conservation mandate shaped a multifaceted project, which would take it beyond its physical boundaries.

The creation of an extensive botanical collection, mainly of cacti and succulent plants, has meant establishing relations with rural communities, scientific institutions and various authorities for the protection of rare species, or those threatened with extinction. This collection is exhibited in various parts of the garden, such as the Conservatory of Mexican Plants and the Area of Rescued Plants. Likewise, the botanical collection forms the genetic base for propagation in the nursery at El Charco del Ingenio.
  The extensive landholding, its extreme topography and the existence of wetlands provide a varied ecosystem, with a surprising variety of flora and fauna. Through the years, indigenous flora has gradually re-established itself in a natural manner, with some inducement, replacing forage grasses and other invasive species. The ecosystem is undergoing a process of healthy regeneration and plants that seemed to have disappeared reappear year by year. The most recent scientific studies made in the area indicate an increasing number of species of flora and fauna, many of them endemic, threatened or in danger of extinction.

Some of the damaged areas of the botanical garden and Parque Landeta have been designated as areas for reforestation with trees and shrubs native to the bio-region, especially those that have been propagated in the garden's nursery and are resistant to drought, poor soils and the extreme climate of this area. They are part of experimental and demonstration plots of an arboretum dedicated to the study of the characteristics and potentials of such species.

These conservation efforts and the promotion of natural resources has received recognition: from thousands of visitors from many different places who come to the Charco, as well as in various publications, and national and international conservation groups and institutions. In 1995, Cante received the National Prize for Ecological Merit from the Mexican government in recognition of its work.
  The size and complexity of the project eventually made it necessary to create a new organization independent of Cante, dedicated specifically to the development of the botanical garden. Therefore a new nonprofit nongovernmental organization was formed in 1998, El Charco del Ingenio A.C., made up of new associates from San Miguel. The nascent organization received in donation all of the land and facilities which make up the botanical garden as well as the valuable collection of Mexican plants, whose care and management was authorized the following year by the Mexican Environment Agency (SEMARNAT) through the designation of the garden as a "management unit for wildlife conservation" (UMA for its initials in Spanish).

The new organization owns and manages the botanical garden, focusing its efforts on autonomy.  With diverse sources of income, it has aimed for sustainable self-financing of the environmental conservation project. It has also built up a trained staff, each with responsibility for specific tasks in the garden (attention to the public, maintenance, propagation, management of flora and fauna, etc.), supported by Mexican college students contributing volunteer social service work, and by other volunteers from many other places.
  One aspect that merits special interest for the new nonprofit organization is the Charco del Ingenio's character as a historical site, an important part of San Miguel de Allende since its foundation. Traces of the past represent an ample compass of time, from remains of pre-Columbian stone tools and ceramics found in caves in the canyon, to a variety of more recent Spanish-era structures, whose vestiges are overgrown with vegetation. Canals, aqueducts, dams, and mills bear witness to skillful water management during Colonial times; there are also ruins of an old hacienda and a still functioning dam, both from the 19th century, and the remains of an iron aqueduct, built in the early 20th century.  
  Along with its primary work of natural resources management, the garden also has a social function as a community gathering place for San Miguel de Allende. In addition to various activities that take place through the year, the garden is the site of the Environmental Education Program of San Miguel de Allende (PEASMA for its initials in Spanish). This innovative program combines values and practices of popular cultural with new alternative technologies and is principally aimed at children and youth of school age in the municipality, who learn about the reasons and techniques for carrying out environmental conservation.

The daily presence of out-of-town visitors, both Mexican and foreign, is complemented by a growing number of local users who come to the site for various reasons - above all, for relaxation in Parque Landeta, an ample and popular recreational space with facilities for hiking, gatherings, picnics and camping.
  Since 2002, the Charco del Ingenio has been a member of the Mexican Association of Botanical Gardens as well as Botanic Garden Conservation International. It has participated in various conferences and meetings, within and outside of Mexico, and collaborates in the Global Strategy for Plant Conservation of Botanical Gardens.

In 2004, the Charco del Ingenio, along with several other places in Mexico, was named a Peace Zone by the Dalai Lama, leader of the Tibetan people and winner of the Nobel Peace Prize, during his visit in the country.
  And in 2005, after years of petitions by the botanical garden, a large area around El Charco del Ingenio was declared by the San Miguel de Allende City Council to be an Ecological Preservation Zone, regulated by a Management Plan and comprising a greenbelt buffer zone where urban development is subject to special restrictions. Thus we seek to preserve this magnificent place as the natural and historical heritage of San Miguel.

The Botanical Garden of El Charco del Ingenio builds itself day by day as a unique and open space with points of interest for everyone: a natural monument, a wildlife habitat, a botanical collection, a historical site, a center of environmental education, and a recreational space for all the community. As envisioned at its inception, it remains an autonomous popular initiative, supported to a large degree by the contributions of its visitors and friends - a silent driving force that helps it to flourish.