It branches from the lower Usumacinta and flows northeastwards, emptying into a complex of lagoons (Viejo, Santa Gertrudis, and El Vapor) connected to Laguna de Términos, a coastal lagoon of the Gulf of Mexico.

The river's flow varies seasonally, generally highest during October and November, and declining from December to June.

[1] The Palizada flows through the Pantanos de Centla, a large permanently-flooded freshwater swamp forest.

As it nears the Laguna de Términos, fresh and salt waters mix, supporting the extensive mangroves.

The mangroves along the lower Palizada are the tallest and best developed in the region, with trees reaching up to 30 meters in height.