The town has a long history as a center for Songhay farmers and Bozo fishing communities, as well as settled elements of the semi-nomadic Fula, Tuareg and Maure peoples.

Goundam was a city of the Songhai Empire, fell to the Moroccan invasion in 1591, and was later seized by Tuareg confederations from the northeast and the Fula of the delta region.

In the early hours of 15 January, Tuareg warriors attacked Bonnier's camp, killing him, 11 officers, two French NCOs, 68 African Tirailleurs, and their interpreter.

A rescue column, commanded by the future Marshal of France Joseph Jacques Joffre, recaptured Goundam on 8 February and Timbuktu four days later.

With highly variable year-to-year rain, the Goundam area has often an unpredictable extents of fertile lands around seasonally flooded river branches, ponds and lakes.