Though it faces no imminent threats, A. atratoensis inhabits waterways with a history of severe environmental pressure in the form of anthropogenic pollution.

Populations exist at both low and high elevations, and have adapted to their respective surroundings; higher-elevation specimens have deeper bodies than lower-elevation ones.

Astyanax atratoensis was first described by prolific German-American ichthyologist Carl H. Eigenmann in 1907, with findings published in the relevant edition of the Proceedings of the United States National Museum.

[4] In the nominal article, Eigenmann remarked that A. atratoensis is closely related to congener Astyanax caucanus, which was named by Austrian ichthyologist Franz Steindachner in 1879.

[8] Though environment can affect morphology, resulting in a deeper body at higher elevations, separate populations of A. atratoensis do not demonstrate differences severe enough to warrant confusion with another species.

[13] Other members of the genus in regions with healthy riparian vegetation tend to be adaptable omnivores that consume plentiful allochthonous material.

Nonetheless, recent action - most notably a court ruling in 2016 - has prompted conservation and cleanup efforts, largely on the part of the Colombian government.