The river -- the world's biggest by volume and which also flows through parts of Brazil, Peru, Bolivia, Ecuador, Venezuela, Guyana, French Guiana and Suriname -- has been hard hit by the drought that has seen wildfires spread across the continent.
"The water level has decreased between 80 and 90 percent in the last three months due to drought caused by climate change," Colombia's National Unit for Disaster Risk Management (UNGRD) said in a statement.
The lack of water was particularly impacting Indigenous communities who depend on the river for food and transport, it added.
AFP has observed boats stranded around Leticia, capital of the southern Amazonas state, in recent days, with large swathes of land exposed by low water levels.
The city, near the borders with Brazil and Peru, is a critical trading post along the Amazon River.
Its residents say this is the worst drought in at least half a century.
Europe's Copernicus Atmosphere Monitoring Service said this week that wildfire activity in South America this year has been "markedly above average" especially in the Amazon region and the Pantanal wetlands.
Fires are burning in Colombia, Peru, Ecuador, Brazil and Bolivia.
Ecuador, which depends on hydroelectric power, is facing severe energy shortages from its worst drought in six decades, and has implemented rolling blackouts and put 20 of its 24 provinces on red alert.
In Brazil, thick plumes of smoke have clouded major cities such as Brasilia, Rio de Janeiro and Sao Paulo, with fumes at times wafting across the border to Argentina and Uruguay.
Colombia's capital Bogota has been rationing municipal water for months.
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