It is navigable through much of its lower reaches, in spite of the shifting sand bars at the mouth of its delta, as far as Honda, at the downstream base of its rapids.

[13] In general, the fish fauna shows connections with surrounding basins, notably Atrato and Maracaibo, but to a lesser extent also Amazon–Orinoco.

[15] The primary threats are pollution (such as human waste, mining, farming and deforestation causing siltation) and habitat loss (such a dams).

[19] The spectacled caiman, green iguana and brown pelican are abundant in these ecosystems but other animal species like the West Indian manatee, Magdalena tinamou, Todd's parakeet, American crocodile, Colombian slider, Magdalena River turtle, Dahl's toad-headed turtle and red-footed tortoise are in danger of extinction.

[23] There are many endangered mammals and birds found in the region, including the brown spider monkey and the endemic blue-billed curassow and white-mantled barbet.

[24] Due to its geographical position in the north of South America, the Magdalena River was since precolumbian times a route towards the interior of present-day Colombia and Ecuador.

During the Spanish colonization of the Americas, the river was the only transport link communicating Bogotá with the Caribbean Sea port Cartagena de Indias and thus with Europe.

In 1825, the Congress of Colombia awarded a concession to establish steam navigation in the Magdalena River to Juan Bernardo Elbers,[25] but his company closed shortly after.