The large population and major industrial base in its watershed have resulted in extremely severe pollution problems for the river.

The Bogotá River is named after Muyquytá, which is derived from Chibcha and means "(Enclosure) outside of the farm fields".

The headwaters of the Bogotá River are in the municipality of Villapinzón, in the northeastern part of Cundinamarca near the limits with Boyacá.

After passing through the municipality of Soacha, the Bogotá River plunges off the savanna at the Tequendama Falls.

It then follows a steep course, falling about 2,000 metres (6,600 ft) in 50 kilometres (31 mi), to join the Magdalena River at Girardot.