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Introduction: Research and diagnosis of water sources is of academic and governmental interest, for this reason, the exploration of numerical tools applied to watershed management, offers the possibility to identify where and what variables are useful in monitoring and rehabilitation programs of aquatic ecosystems. Environmental planning and management, which includes water quality, is conventionally analyzed by physical, chemical and hydrobiological indexes. In 2014, through the water management guide, included the assessment of the ecological quality index (EQI); it was generated a comprehensive approach through a numerical system of correlations that diagnoses, classifies and detects environmental impacts. Objective: This research aims to demonstrate that the EQI allows to assess the quality of aquatic ecosystems affected by different environmental situations. Methods: In order to analyze the application of this tool, we studied three scenarios located in different biogeographical regions of Colombia and, as a hydrobiological group indicator, we used peripheral and phytoplankton algae. The ecosystems were monitored between 2007 and 2015 and correspond to a flood plain, a high mountain Andean river and a group of water stream in a tropical humid forest. Results: Canonical correlations were significant (P < 0.005) and a model of weighted averages, allowed to estimate the optimum and the tolerance of each taxa for the sites ecological classification; variables related to ion concentration, acidity damping, temperature and hydraulics, influenced the models that explained the abundances distribution of the studied biological groups. Conclusions: The application of the EQI makes it possible to identify variables, organisms and numerical systems to classify ecological status. These results are useful in the diagnosis and monitoring of aquatic ecosystems and that can be implemented in other scenarios. [ABSTRACT FROM AUTHOR]