It originates in the Eastern Ranges of the Colombian Andes in Piedecuesta and flows through the northern part of the department of Santander into the Magdalena River in Puerto Wilches.

The Lebrija River originates at an altitude of 2,532 metres (8,307 ft) in the Eastern Ranges of the Colombian Andes to the northeast of Piedecuesta, Santander.

[10] The heavy rains over the capital district of Santander, the metropolitan area of Bucaramanga, have caused mortality of fish in the Lebrija River.

The rainy seasons are March to May and September to November with drier periods from December to February and June to August.

[15] The following species and genera are noted in the upper part of the Lebrija River: Ocotea sp., Miconia sp., Guarea grandifolia, Hedyosmum bomplandianum, Guateria sp., Protium sp., Ochroma sp., Piper sp., Trema micrantha, Vismia baccifera, Urera caracasana, Cecropia sp.